So, I’ve installed Avast onto D:\Program Files (x86), not sure why I did this, and its mixed in with all these other Folders (Games and other programs). Now when I try to uninstall it tells me to make sure which folder Avast is in as it will delete the entire folder. Is there a way to uninstall Avast Free (I intend to re-install it into a separate folder) and keep my files intact?
Cheers
Take backup before you do 
As in a disk image.
Ok I dont have a HDD with enough free space. Could I just System Restore to last week?
You can try but, there are no guarantees when it comes to a Restore Point.
That’s the reason an image backup was suggested.
If you have an HDD with very little free space, there may not be enough space to do that. Windows generally looks for 15% free space to do things like defragmentation.
Before doing any of this below, what is your Operating System version ?
But about your original point about avast uninstall:
The folder Avast is talking about is the D:\Program Files[b]AVAST Software[/b] folder, not the complete D:\Program Files folder.
I have uninstalled avast on a number of occasions and it has only removed the C:\Program Files\AVAST Software folder, where it is installed on my system, it hasn’t removed the whole C:\Program Files folder with all of my other programs, see image example attached. But it is important to point it at the correct folder location, D:\Program Files\AVAST Software, in your case.