How to Do a Clean Install of Windows Without Losing Your Files, Settings, and Tweaks

How to Do a Clean Install of Windows Without Losing Your Files, Settings, and Tweaks:
There's nothing like a fresh install of Windows to clear your mind, but it comes at a cost: you have to set everything up again, just the way you like it. Here's how to reinstall Windows, migrate your important settings, and leave the clutter behind.
You don't have to regularly reinstall Windows just to keep things clean, but that doesn't mean you'll never have to do it again. Maybe you just bought or built a new computer, or maybe you didn't take care of your computer as well as you thought and you have to do a clean install. Maybe you just want to wipe the slate clean for that new, fresh feeling. A clean slate is nice, but it also means you're going to spend the rest of the weekend setting up all your old programs, settings, and system tweaks, half of which you've probably forgotten because you set them up so long ago. Here, we'll go through some tips on how to back up your most important settings and tweaks, and restore them on your new system.

Part One: The Preparation

Before you reinstall Windows, you're going to want to go through all your stuff and back up the programs, settings, and tweaks you want to take with you. Here's what we recommend.

Step One: Export a List of Your Programs

Before you do anything else, it's handy to have a list of all your currently installed programs so you know what settings to back up, and which programs you want to reinstall later on. The easiest way to do this is with CCleaner (a program everyone should have installed). Just open it up and export a list of your programs:

1. Open up CCleaner (you can do this quickly by right-clicking the Recycle Bin and choosing "Open CCleaner" from the menu).
2. Head to the "Tools" section in the left sidebar.
3. Click the "Save to text file" button in the bottom right-hand corner, and choose where you want to save it.

Save the file in your Dropbox or on a USB stick so you have it after you do your clean install.

Step Two: Back Up Your Windows Settings

Next, you should back up any Windows settings you can so you don't have to do too much tweaking after you reinstall. The best way to do this is with Windows Easy Transfer, Windows' built-in migration program for just such occasions. It can back up app settings too, but it's not very good at it, so we aren't going to use it for that today.
To start it up, just open the Start menu (or screen) and type Windows Easy Transfer. When it pops up, you'll get a description of what it can do. Click Next and choose an external hard disk or USB flash drive for your files. Tell it that tihs is your "old" PC, and it will scan your users for items to back up. Click Customize to tweak the selection. In this case, we recommend unchecking everything and just backing up "Windows Settings," though you can use this to back up your documents and files too (see below).

Step Three: Back Up Your Documents and Files

Before you reinstall Windows, you'll obviously want to back up your documents, music, movies, and other files just like you always would. I usually just copy these to an external drive or move them with Windows Easy Transfer as described above, though if you back up your computer regularly (which you should), you can always just restore them from your backup later on as well.

Step Four: Back Up Your Program Settings

Next, you'll want to back up all the settings you've worked so hard crafting on each of those programs (at least the ones you plan to keep). Different programs store their settings in different places, but here are the main places you should look:
Your AppData Folder: This folder, located at C:\Users\yourusername\AppData, is where the majority of your programs store their settings (usually under the Roaming subfolder). Usually you'll see a folder with the name of the program or its developer, with a number of files inside. You'll want to back up the program's entire folder.
Your "My Documents" Folder: You know where this is already. If you open it up, you should see a few folders for other programs on your system, which often contain user settings or tweaks that you'll want to save. Back those folders up individually, just like the AppData folders.
Your Program Files Folder: Most programs won't store settings in the Program Files folder, but it might store other important stuff, like plugins or themes you installed after the fact. If that's the case for the program in question, it's a good idea to back up its folder in C:\Program Files (or C:\Program Files (x86)) for good measure.
Your Registry: Some programs, like Fences, store all of their settings in your Registry. This is pretty easy to back up: just press the Windows key, type regedit, and press Enter. Navigate to HKEY_CURRENT_USER\Software and scroll down to the program in question—in Fences' case, under Stardock\Fences. Right-click on the program's folder in the registry and choose Export to back it up.
Games: If you play any games, the above tricks should work, but we recommend using a program like GameSave Manager to make the process infinitely more simple. It'll search for games on your system, find where their save files are stored, and back up everything for you.
Again, different programs will store settings in different places, so if you're unsure, do a bit of research before you start. If a program has the ability to "export" or "back up" its settings to a file, that can be handy as well.
Once you find the folder(s) in which a program stores its files, copy that folder to your Dropbox or a USB stick. I also like to put a text file with that folder indicating the path to where it was stored. For example, if I were to back up Pidgin's settings, I'd back up the .libpurple folder in my AppData and the Plugins folder in Pidgin's Program Files. I'd then create a text folder that noted where each of these two folders came from, so i know where to put them when I restore them later on.
Repeat this process for each of your important programs, and you should have everything you need to reinstall them later on without losing your settings. This sounds like it'll take awhile, but it shouldn't—it only took me a few minutes to back up all the important settings from my favorite programs.

Step Five: Create .Reg Files For Your System Tweaks

If you're an intense tweaker, you've probably edited the Windows Registry to enable some awesome under-the-hood power-ups, like hiding items in Windows Explorer or speeding up the Windows taskbar. The easiest way to back these up, says Justin Garrison, is to save a .reg file for each tweak in your Drobpox or USB stick. That way, whenever you reinstall Windows, you can just double-click on your .reg files to install those tweaks instantly.
You can't necessarily create a .reg file for every tweak—just the ones for which the registry keys in question already exist—but that can still cut down on a lot of research time. Google around to see if someone's already created a .reg file for the tweaks you want (they probably have), or you can do a little research and create the file yourself.

Part Two: The Restoration

Once you've got everything backed up, it's time to reinstall Windows. Insert the Windows installation disc and boot up from it, or use Windows 8's Reset option in the settings to start from scratch. Once you've got a fresh installation of Windows, it's time to restore all your stuff.

Step Six: Restore Your Windows Settings

Before you do anything else, it's a good idea to restore those Windows settings we backed up earlier. Reopen Windows Easy Transfer on your fresh install, plug in your USB drive with your saved transfer files, and this time choose "This Is My New Computer." It'll restore your Windows settings and your user account that you backed up, along with your Windows settings so you don't have to find them all again.

Step Seven: Reinstall Your Programs

Next, it's time to reinstall all your programs. This can take awhile, but you can speed up the process with a few tools:
Ninite: Ninite is still one of our favorite tools for installing programs quickly. It doesn't have every program out there, but it's a great start. Just check off all the programs you want, and Ninite will create an all-in-one package to install them in one fell swoop. Be sure to check out the Lifehacker Pack for Windows, too, which has its own custom Ninite installer for our most recommended programs.
Chocolatey: If you're more of a command line geek, Chocolatey is a handy utility that brings Linux-style package management to Windows. With a few well-placed commands, you can install a ton of programs at once, bypassing the need for all those separate installers. Again, it doesn't have every program imaginable, but it does have quite a few to get you started.
Portable Apps: If you're tired of downloading installers all the time, you might want to try using portable apps instead. Portable apps essentially let you carry all your programs and settings over to another computer with no installation required. You'll still have to search out each app yourself, but after you do it once, you'll never have to do it again—every clean install from here on out will be much quicker because you'll already have half your apps ready to go. Check out our guide to portable apps for more information.
Once you've installed the bulk of your favorite programs, you may need to open up that text file we got from CCleaner earlier to pick up any stragglers that aren't in Ninite. Install whatever you want, and when you're done, move onto the next step.

Step Eight: Restore Your Documents and Program Settings

Once you've reinstalled your favorite programs, you should restore your documents, music, movies, and other files (in case any of your programs depend on them—like iTunes, for example). This should be pretty easy: just restore them to the same place they were before (e.g., put your music back in C:\Users\yourusername\Music\iTunes\, or wherever you had it located).
Do the same thing with the app settings you backed up earlier. Open that folder and restore the folders to their original locations in AppData or Program Files (in the case of AppData, you should overwrite any files that are already there). When you start that program, it should inherit all your old settings and it will be like you never left!

Step Nine: Restore Your Registry Tweaks

Lastly, restore any registry tweaks you had. That means double-clicking on your .reg files that had app settings or Windows tweaks stored inside, and redoing any registry tweaks that you couldn't put into a .reg file. Remember, you may need to restart the program in question (or restart your computer altogether) for the registry tweaks to take effect.

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It seems like a long and drawn-out process, but you'd be surprised. I had all my settings copied over in a few minutes, and was up and running with most of my favorite programs not too long after reinstalling—it's much, much faster than setting everything up from scratch. Of course, if you like setting everything up from scratch, feel free to do that too. This is just a great compromise between doing a fresh install and keeping all your settings that you don't want to set up again.