Although .md was a VERY old copier format, it fell into disuse compared to "SMD" (interleaved) and "BIN" (raw, untouched dump).
As has been mentioned, if you got the ROM from a No-Intro set, then .md is probably just .bin renamed (as No-Intro opted for using a less generic extension for MD ROMs).
If you're using that ROM you converted from "md" to SMD, then you already messed it up.
Either convert it back or delete and redownload the ROM from wherever.
Genesis ROMs don't have headers. SMD vs. BIN is the only issue. SMD format is messed-up enough that people PROBABLY wouldn't ROM hack in it, meaning "BIN" should be the right format. (again, a No-Intro "md" file is a "BIN" renamed)