Some sort of bulk rename tool might work.
EDIT: In linux, what about the following cli solution:
Code:
find -regex '\./.*\.\(azw3r\|mbp1\)' -exec sh -c 'for x; do ext=${x##*.}; needdir="${x%.*}.sdr"; fname="${x##*/}"; mkdir -p "${needdir}"; mv -- "${x}" "${needdir}/${fname}"; done' _ {} +
If you use Windows you just need to install
Gow and use gfind instead of find, or use cygwin, or find your own solution.

It seems from google that your average bulk rename program does not support creating directories, and I have no patience to find a windows batch/powershell solution (I am terrible at either).
Credits to
http://unix.stackexchange.com/a/24141 and good ole trusty
http://tldp.org/LDP/abs/html/string-manipulation.html 
(I am slowly getting the hang of it...)