What do you do If the whole extruder is clogged?
I have a prusa 13 that's shipping in the mail, and I intend to make good use of it, one also own a da vinci jr. and the one time it got so clogged that the extruder itself was filled with pla, with that said I replace the extruder, for the da vinci, but besides that, as for my a prusa, what should I do if the extruder, not the nozzle gets clogged that badly?
If you are good at being patient and extremely careful, you can clean out the feeder tube by using a small drill, manually operated. Use a bit with diameter smaller than the filament in use.
I recommend first removing the nozzle. Then,from the top, hold the drive gear open and gently work the drill bit down, removing often to clean off debris. If the bit is long enough, sooner or later it'll project out the hole where the nozzle fits. If not, gently work from the bottom up.
Since you have the nozzle out, it's easy to see if there's gunk in the upper chamber of the nozzle; either drill that out or use heat-methods to liquify, and clean out with any soft tool.
Usually any clog in the narrow orifice can now be removed by re-assembling, heating the extruder head to operational temps, and pushing the remaining gunk out simply by guiding fresh filament all the way in. I do not recommend trying to use a micro-drill bit as that can easily damage or open up the orifice. If you can get a piece of stiff wire (e.g. 0.375 for a 0.4 nozzle), try that once the head is at operational temperature.