So I try and measure my extrusion length and calibrate the E-steps on my Prusa i3 with a bowden setup. I have abs filament in right now and when I try to extrude 100 mm it only extrudes 60 or 70. But when I take the filament out of the extruder and I extrude by 100 mm its about exactly 100 mm. Could it be that the extruder is clogged or getting cold too fast? Because right now my prints come out OK, but the layer adhesion and walls have some holes in them. Any help would be appreciated, thanks!

How can it extrude 100 when the filament is not in?

Sorry, should've made it clearer, I meant that the filament is fulled from the extruder, I solved the problem now by actually putting the filament in while calibrating the E-steps.

You may be suffering friction in your bowden tube resulting in reduction in extruded filament. Does your extruder click or strip the filament with the bowden tube attached? Ideally you want the idler tensioned to click rather than being tight enough to grind the filament.

Check your filament diameter in multiple places to ensure it is not oversize and from multiple directions to find out if it is oval.

You could set your esteps higher or ditch the bowden extruder I've found them to be very unsatisfactory.