layer within a layer

I have a graphic and illustration class in high school. What I do to organize my work is to put layer with in layers. In example if I'm doing a body project. I would have fingers in one layer, hands in one layer, and arms in one layer. Then they would all be in one layers call right hand. However my teacher insist that I do not put layers in layers. So if I'm doing a really complicated work I would have 100 layers or so and I would have to scroll up and down forever to find the layer I'm looking for. To me it's a much simpler way of working. What's your opinion on this?