Alright, I've got a mid-tower case, a Corsair. Specifically, this model.
Inside, I have the motherboard, CPU, GPU, one HDD, an optical drive, a Cooler Master Hyper 212 on the CPU, a Miyamoto Musashi on the GPU, one 12cm fan in the front, and one 9cm fan on the left side (looking from the front). All in all, there are a lot of wires; the PSU is a Xilence RedWing 580, which isn't modular, so there are cables flying everywhere. I've tried to manage the wiring as best I can by taping them to the walls and tucking them away, but it still looks pretty messy.
I've looked at some guides on how to tidy up cables, but my biggest issue right now is that the motherboard tray extends across the entire right side of the case (again, looking from the front), meaning I can't tuck the wires anywhere without them being visible.
What I want to do is measure the space to the right of the motherboard and drill a hole there so I can route the wires behind the tray. How feasible is this? What kind of tools would I need? I assume the case is aluminum.
Here's a photo to clarify:

If we assume the blue lines mark the edges of the motherboard, then I would cut out the section marked in red. Obviously, it would look cleaner than this sketch. I'm not using the vent area because it's impractical for me, and please ignore the dust and the wires—I was running some experiments while my parents were out xD
Do you have any other advice? Anything else I should keep in mind?