M3D Micro printer stops extruding but is not clogged
I'm not sure how similar the two systems are, but I use a Stratasys uPrint SE Plus and I've run into a similar problem. 

There are two rollers in the head that pull the filament through to the extruder nozzle, and in one instance they appeared to have heated up, melted the filament enough to create two "indentions" on either side of the filament, making it such that the rollers had no purchase on the filament itself. There was never any clog, no material feed error, but it was still failing to print. Wound up having to replace the head altogether.

Again, not sure how similar the extrusion mechanics are in the M3D, but suggest checking the components that actually advance the filament, and the filament itself.