In an earlier post about MakerWare 2.2.0, I showed what the new raft is like. As I continue to use it, I am enjoying the speed and simplicity of using MakerWare to generate "every day" prints.
One of the best features is, I think, the raft. With the new raft handling, I can pry the raft off without too much effort. I just work a spatula underneath the object and twist - a motion similar to shucking an oyster.
The solid layer at the top of the raft should allow the raft to come off more cleanly than the way rafts were done before. If you find that your raft is sticking to the object, it's very likely that you are over-extruding and the raft is fusing to the object. I haven't had this problem when using our high-quality 1.75mm filament. But if your filament is too thick, you certainly could have this problem.
If you are over-extruding (or under-extruding) throughout the print, you can adjust that by playing with the Makerbot Slicer options documented at http://www.makerbot.com/support/makerware/documentation/slicer/ :
Specify the diameter of the filament you will be using. If this value is too low, your extruder will extrude too much plastic. If it is too high, your extruder will extrude too little.
The other possibility, though less likely, is that your bed is way too close, causing the first few layers to be jammed more tightly together. If your print is otherwise looking very good, try adjusting the Z-height offset -- that may be all that you need.