I had the same problem with my rear MC. What you got out is the pushrod and the piston is stuck up inside. Probably looks like this first pic. I put some penetrating fluid and let it sit for a while. Nothing. Heated the whole thing with a heat gun. Nothing. Took a screwdriver and pushed down hard on the piston and it moved in about 1/4 inch. Nothing. Decided to leave it till morning and when I set it down the piston popped out.
I think I would try the penetrating oil and maybe try shooting in compressed air through the outlet port. Have the cap on the reservoir. If that doesn't work try my technique ( I think the additional compression on the spring did it). As a last resort I was going to drill a hole into the piston for a screw and pull it out with that.
As for the front make sure you get the wire clip that holds the boot in place out as it will sit on top of the c clip. Once that is out find a way to hold down the piston as this will take pressure off the c clip and make removal easier. You need a deep reach c clip pliers and you won't find them at hardware or auto stores. mikesxs.com has them for around $10.00 or do a search and see how others have done it with modified tools. I filed down the tips of a long needle nose pliers. If you are in no hurry the $10 spent and a few days wait are less aggravating than the alternatives. You can see the wire boot clip in the second photo of the front MC internals. Third pic is the rear MC internals.