MRD Troops can be found on Mission Six "Priorities" - they come in an assortment of enemies from ones that melee with some elemental powers, levitate shooting pulse shots, and ones that look like an abomination (miniature form of the John Sublime boss).
If you want to grind these enemies there is a Challenge Area if you have good standing with the Brotherhood. During the sixth mission after rescuing Caliban and talking to Northstar, you'll come across Juggernaut and you'll have the option of accepting his Juggernaut Smash-Up mission. If your faction standing is more so on the X-men side you may have to do another playthrough on a new game+ siding with the Brotherhood if you have not already in order to play this challenge mission. Once you have cleared the mission, you can replay it anytime by going to the load menu and selecting your character with the challenges available, it should be Challenge Mission #14 on the bottom with Juggernaut's image on it.
Within this challenge, you are to smash-up the objects that blink in order to finish it, however there will be an infinite number of respawning MRD troops coming out to be fought. After five hundred of them, the achievement is yours.