I need some help with preparing CDs for manipulation. I want to drill a larger hole in the center so to help with ease of palming, etc. The problem is I have tried to do it myself but I find the holes are not centered. Any suggestions? Help?

What sort of drill bit are you using?

I find that just filing the hole out works quite well, not as quick as drilling but does give a neat result.

The problem that I have is I have no way of holding the cds down. I want to make the hole to about 1" dia. Plus, I want the holes all the same so they stack together neatly.

Make a centering jig to hold the CD in place and use a key hole bit with a pilot bit.
We are talking drill press aren't we?

I use a dremel. Use a marker to draw the 1"diameter hole. Drill off the desired hole by melting the plastic using high speed. Sand or file to smoothen the edges.

Use a drill press of they sell extended drill bits at the hardware store, go shopping. Stack the disc and tape together. Place on a block of wood. Drill in graduating sizes. Plastic does not like to be drilled all at once with one size. The bit will tear up the material.

You are having a problem with centering. Isn't the original hole in the center, use the for a guide. Now drill bits are expensive and you will have to buy several sizes from the current size to the desired size you want in the end.

Get a pipe reamer. Don't even think of doing it simultaneously. Do them one at a time. Then touch them up as a stack. And work slowly.