You can't get rid of the Folders C:\Program Files [on both 32-bit and 64-bit Windows] or C:\Program Files (x86) [for 32-bit programs installed on 64-bit Windows], part of the Operating System. But a number of those in the Program Files (x86) Folder should be uninstallable and reinstall on D:, don't necessarily have to be in Program Files (x86) Folder on D:, can be in their own/default install. Same for those in C:\Program Files, many can be installed on D: in their own/default Folder.
The main thing about the uninstall/reinstall process is that most Windows-based programs do more than one thing when installing, copy its files to a Folder, create the icons in the Start menu, copy support files into C:\Windows or its subFolders and most importantly make Registry entries so Windows knows how to run the program/s. Simply moving program files can break the process and Windows may not be able to work with them.