MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
I have had this issue before, more than once, and the video below is a good place to start. As long as your hotend still gets hot, you should be able to melt the filament enough to push the clog though. If not, replacing the hotend is not that difficult, it feels scary at first because it's a $200 printer that you don't want to mess up but they are fairly sturdy and well made.
Over time you WILL have to replace the hotend (it gets really hot and will wear out). I have had to replace the hotend on multiple types of printers and the M200 is the easiest.
One thing I have found that helps to prolong the life of a hotend as well as prevent clogs is to push a bit more filament though the hotend after printing and then retract the filament out of the hotend. This can be done manually, or you can add some gcode to the end of the print file to do it for you. Unfortunately I don't have the end gcode on hand so I can't just give it to you, but it wasn't hard to figure out; google.