Basically, yes. You can run FPCMD.EXE, which is supplied with the
Windows version of F-PROT. It is a command-line program, but without a
user interface; you use command line such as
fpcmd c: /auto /disinf /packed /server /report=c:\virus.txt

Commands are the same as F-PROT.

F-PROT works fine to check, say, a single file or directory under Win
NT/2000/XP/2003