Cooler Master Hyper N520 CPU Cooler

I suggest you take your side panel fan and put it elsewhere in the case if possible. When I installed my Xigmatek CPU cooler, I moved my side fan to the bottom of the case, so there's no interference now.
 
It's never a good idea to modify the heat pipes in any way. As Marshillboy suggested, moving the side panel fan is your best bet.

You could even look into getting a slimmer fan. This one is 12mm thick which is only half as thick as regular fans (25mm): Scythe SY1212SL12L 120mm Case Fan

 
Yeah, don't cut heatpipes. You do that, and your heatsink will become a paperweight.
 
Sorry, but what exactly is wrong with just taking that top protruding section of heatpipe off? it doesn't look like it's even doing anything up there =/
 
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