With terminal, start it up.
1) cd Desktop
2) type ls then return, you'll get a listing.
3) I'd then do mkdir temp which will create a folder named temp on the Desktop.
4) study the listing and selectively move files into the temp directory.
For example, I've got some .dmg files on my desktop. So I'll do a mv *.dmg ./temp. Rinse and repeat.
I wouldn't do them all right away, you may wish to create some more temp folders to help you organize your work, like temp1, temp2 or any name which helps you organize.
Once you get the number of files/folders down to a reasonable number you should be able to use Finder again and finish your reorganization