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.
The extruder is not a single component, but a collection of components. From the top, you may have a bowden tube or a direct feed type of design. If the former, there's the bowden tube which extends into the heat sink. If it is a direct feed and not an all-metal design, there will be PTFE tubing inside the heat sink.
The heat sink is a finned assembly, usually cylindrical, sometimes other shapes. Attached below that will be a threaded coupling called a heat break. Both the heat sink and heat break will be configured to have the same inside diameter, to allow the filament to pass through to the next stage.
The heat break passes into the heater block. The nozzle passes into the heater block from the opposite side. The two items contact each other when properly assembled.
If your nozzle is not blocked, but there is a blockage somewhere else, it would indicate that the PTFE tubing has become damaged or a piece of debris has managed to fall into the opening when filament was removed.
The items are easily disassembled and the pathway for the filament can be cleared with a suitable tool.
If a portion of the extruder assembly has previously filled with filament, the nozzle was not solidly secured to the heat break, or the PTFE filament had slipped back or was not fully inserted into the heat sink.
Typically, any unclogging technique involves melting the plastic around the piece of debris causing the clog (what happen next can differ, depending if you are using a needle, cold pulling, or a total disassembly of the extruder).
If the clog is localised to the hot end, one can usually achieve the melting via heating the nozzle as if one were to print. Clogs that are not localised at the nozzle, are usually a symptom of a severe malfunction of the printer (damaged PTFE tube, loose assembly, broken parts...) and - while unclogging is still of essence - they should be investigated further.
In case of clogging that is not localised at the hot end, chances are you will be able to disassemble the extruder in its components (heat sink, heat break, heat block, nozzle, etc...) while cold, and clean each part mechanically, possibly having administered some heat.
Should the cold disassembly not be an option because some parts got stuck together thanks to the molten plastic having acted as a glue, use of an external source of heat may be required (just heating up the nozzle wouldn't probably work, as the extruder is designed to prevent heat propagating above the heat break). Many people use a butane torch or a heat gun in these cases, and proceed to the complete disassembly of the extruder while hot.
If using an external source of heat, be mindful that torches and heat guns could very easily over-heat the extruder, and damage it (so: make quick passes, and stop heating as soon as you can see/feel the plastic melting). Also cabling and other electronic components (e.g.: thermistor) could be easily damaged, so it is advisable - if possible - to remove them from the assembly prior to heat it.
Disassemble the hotend (always disassebble when hot), When you seperate the heat block, nozzle and the heat sink parts of the extruder if you are lucky the parts clogging the non-nozzle areas will be easy to pull out.
Replace the nozzle, nozzles are cheap and not worth worrying about.
The heat block should be clear because, in most hotend I know about, the filament should transfer from the heat break to the nozzle without touching the heat block directly - if this is not true in your model then it's the same as for the heat sink below, if there's plastic where there shouldn't be you didn't screw the nozzle of heat break (or both) all the way in.
If the plastic doesn't come out of the heat sink easily it's time to replace the teflon tube if there is one, in an all-metal hotend it's possible the inside metal tube is damaged and you need to relace the hotend.
In any case, if the plastic doesn't come out with just a tiny bit of force stop before you damage anything, heat the componene to above the melting temperture of the plastic and then try again.