<p>I have Prusa i3 derivative with MK8 extruder and Marlin 1.1RC8 as firmware. I already reduced the default speeds as well as the accelerations. But sometimes when trying to print with BQ PLA filament (220°C), mostly during filling areas, my extruder clicks. The below screenshot of Slic3rs Layers view shows the clicking "lines".</p>

<p><a href="https://i.stack.imgur.com/Rzmxn.png" rel="noreferrer"><img src="https://i.stack.imgur.com/Rzmxn.png" alt="enter image description here"></a></p>

<p>What settings I need to change to avoid the overextrusion in this case?</p>

The only time that I've observed clicking from the extruder on my Anet-A8 is on the first layers when I have the head height set too low - the nozzle is unable to extrude at a high enough rate to allow the filament to progress as requested.
If you have a somewhat repeatable scenario, you could try reducing the filament feed rate to 90% or so, and see what effect that has. I have already observed with one of my reels of filament that 90% feed rate gives me a less over-filled solid area, so maybe the default feed rates are a little on the high side (or this filament is of excessive diameter).