I looked at a couple threads but found nothing conclusive. One of the small oval covers on either side of the ebrake has fallen down into the console.

I have a 2004 Cooper S 5 speed if that matters. That hole that is no longer covered is driving me bonkers!!!

 

A little late, but I just did this and found this thread while searching.
Here's the answer, for any other searchers.

- To remove the console:
- Squeeze sides of ebrake boot together and wiggle it out (tougher than it sounds) Start in the middle and work out.
- Remove screw from just behind ebrake
- Pull console up, the rest is held by four clips (the 05/06 has a screw in the cupholder

 

A+

 

I recently removed my handbrake boot and broke some of the clips.You should push down and then inward to release them,the front has a tab that slides in.I think there were four clips on each side and two at the back so if you work your down each side then the back to release the clips then pull the boot up and to the rear you can avoid my dumb mistake.Fortunatly even though I broke some clips it still popped back in ok and seems fine.