Crankset removal, Shimano FC-M361
I think what is confusing you is that the square hole cannot be seen in the crank with the retaining bolt removed. It seems this model of crank has a circular flange at the outboard end of the square hole for the bolt head to bear on. 

Regardless of what the axle-crank interface is, the cranks are removed with a  crank puller tool that threads into the retaining bolt hole in the axle and the larger threads in the crank, and pulls the two apart. 

DO NOT attempt to get the cranks off any other way, you will damage the square taper interface in the alloy crank arm. (Someone asked a question here once who had levered his cranks off with a crowbar, and totally trashed them.) 

You also need a special tool to remove the cartridge bottom bracket. There a ton of help available on the web. Personally I think Park Tool's pages and youtube videos are the most detailed and comprehensive.

Removing 3-piece cranks

Removing cartridge BB