if the program your trying to run is a console based program only then this is what you do.

click start, run , type "cmd" (with out the " ") press enter then. run the md5 program.

i use helix for checking the md5 normaly.

make sure you put the program in c:\windows\system32

and then you should be able to cd to any folder and use this program you may have to tell the program were the iso file is.