In a BRP game, a character will have some stats (STR, CON etc) that are 3-18 based, with these stats affecting subsequent percentile skills. MD has 10 percentile stats (Attack Skill, Knowledge, Persuasion etc) that are fairly broad.
BRP has percentile skills, either broad or narrow (Combat or sword). MD has a range of professional "skills" that range from rank I to rank VI and are fairly all encompassing. These either provide a bonus to stat tests, a fixed bonus to combat etc or else allow the character to automatically do certain tasks based on the rank.
Combat is fairly similar in both, with roll under, an attack and defence roll, normal and crit/fumble results and separate damage roll. They both have hit points, although on a different scale, and armour reduces damage in both.
Magic is completely different in both, with BRP having various spell lists and MD having freeform magic based around the manipulation of probabilities.