Why are molecules somtimes attain three-dmensionl spapes rather then flat?

Answer 1

If I understand you correctly, electrons are negatively charged. Because opposite charges repel each other, they want to be as far apart as possible and they can only do this if they form three dimensional shapes.

Answer 2

Yes the molecules will want to be as far apart from each other as possible you can figure out the angels using really anvanced geometry, for example, the most stable shape for cyclohexane is liek chair shaped!