Create subdirectories under the main one. Call them something like A and B ... Then open a command prompt window. Change directory to the main one (cd \main or whatever). Then use the move command to move all files starting with "a" to the A subdirectory (move a*.* A). Do the same with all files starting with "b", moving to B subdirectory, and so on. After they are separated, you may find a way to group them better.
Another method that would take longer is to open a main vi and look at the VI Hierarchy to see which sub-vi's it uses. Create a subfolder and move these sub-vi's and the main into the new subfolder. Do this for all main vi's. This will take a long time but it will organize your vi's in a good manner. If some sub-vi's are used by more than on
e main vi, you might want to create a subfolder called Common or Support or Library or whatever, and move the commonly used sub-vi's there.
Good Luck, this will be tedious and time consuming.