Under- / Over-extrusion
The firmware of the printer controls the speed of the Bondtech extruder gears rotation (among other things) – that’s how the printer pushes the filament out of the nozzle.
Each profile in the Slic3r PE app contains settings that determine how much filament the 3D printer should extrude. However, because the 3D printer does not provide any feedback on how much filament actually leaves the nozzle, it may be that less or more filament than the firmware expects. If that happens, you may notice gaps between (or in) layers. An excessive extrusion will also negatively affect the surface finish of the printed object with small blobs or bumps.
The most reliable way to test whether your printer extrudes an incorrect amount of filament is to print a simple 20 mm high cube with at least 3 solid layers at the top and at the bottom. You can tweak these settings in Slic3r PE “Print Settings” tab. At the top of the cube, make sure that the 3 top layers are firmly connected. If there are gaps between the three layers, then it means the extruder is not pushing the right amount of filament. If you find that your printer has an insufficient extrusion, but your extruder is not clogged and the thermal cooling for the extruder is sufficient, there are possible issues with the flow.
To fix this problem, try increasing the Flow value. Press the knob to open the LCD Menu, go to Tune and select Flow. Then rotate the knob during the printing process. Anti-clockwise = decrease the amount of material, Clockwise = increase the amount of material. The best option is to try changing it by small steps. Increase or decrease the flow by single numbers and see whether the nozzle will start extruding enough filament when printing your model.