Most filing is done by last name, so Kim, James J. If the M.D. is actually relevant, I suppose I'd label the file as Kim, James J. (M.D.). You should really ask whoever is in charge of the filing system, though.
I think it varies based on your system. Filing is typically ordered by last name, but as for labeling it, or in which order the title suffix goes, that will depend on the policies and practices of your workplace.
For example, some people change the M.D. suffix to the Dr. prefix when doing this.