As Ahmed points out in the comments, Windows sort of autonumbers a process for you by creating a process ID and this could be used to differentiate between them. The problem is that process id isn't sequential like you have here. You could sort them by process id and assign your own numbering but if one process quits the numbering changes for all those processes after it, which could be a problem for you. You could always start the processes, retrieve their IDs and maintain the mapping of 01 is process ID x, 02 is process ID y etc yourself and pass it round your program
You could also consider to start each app with command line arguments, that you can later retrieve with one of the techniques mentioned here so when you three times launch your exes you could:
for(int x = 1; x <= 3; x++)
Process.Start("example.exe", x.ToString());
Example should be capable of ignoring the dummy argument, though. If it will heed it, find some way to make it a no-op
If all this fails, maybe just having 99 copies of the same exe, names accordingly, in a folder and ready to go would be the simplest trick