Then use the pill bottle as your mold positive. The dimple in the bottom will already be there.
That's what i did with GE Sillicone II. Might not last years but at $4. for a tube, you make two mold.
Get a 2" x 3" pill bottle
Take modeling clay, and make a 5"x5" base about 1/2" thick
Put your bottle in the modeling clay openind down and jam it in there until it's flat .
Put over that a 3" diam. x 4" PVC or other material pipe and put some wax on the inside wall.
Jam this over the pill bottle in the modeling clay. Make shure to center it.
Fill the gap bettew the bottle and the pipe with sillicone and cover the top, making sure that you don't create air pocket. This shoud give you about 1 inche wall and bottom.
Let sit a week or more. No rush there.
Demold. This can be tricky and you may have to use a small saw to cut the pipe on two side and split it open.
Hope this is clear enough..