Ok, I found a very creative way of removing the rectangular and the lines from the mini-map. Basically I used the ping model, because ping model is always on top of the mini-map. So I edited ping model in the model editor, created trigger that runs when menu is enabled to ping the mini-map. Thus successfully hiding everything under the ping to black.
Also edited the upper interface to be black. As crappy the interface handling and editing in Warcraft 3 is, it's always nice to find limited workarounds.