Extruder Making Thudding Noise

I have a Prusa i3 that when I print the first few layers there is a thudding noise from the extruder being too close to the bed. The problem is, when I lower the bed to the point where the noise stops, the extruder is too far from the bed.
If someone could help tell me how to fix this that would be great, thank you!

Does your extruder idler bearing turn freely? Is your stepper current adjusted correctly?
Your extruder motor seems to be skipping, causing the thudding noises when the nozzle is lowered. Try pushing filament through the hotend manually with the nozzle in the air to see if there's significant resistance. This might be preventing the extruder from putting out plastic against the additional resistance of being lowered on the bed.
Also, what are you printing on? It's possible that your nozzle is at the correct height but the surface you're printing on just has bad adhesion.