Consider NOT cleaning your gravel at all! I rarely "clean" gravel. I have
done so when I had a cyanobacteria (blue-green algae) infestation that I
thought was due to too much left-over food in the substrate. (II used to feed
bloodworms a lot, and they seemed to cause this type of algae/bacteria outbreak
if I let too much fall in a single spot that did not get eaten.) Although the
vaccuming helped in this case, I have found that with more careful monitoring
of my nitrate levels, cyanobacteria rarely bothers me any more even if there is
a bit of a food build-up.

For the most part, your plants should thrive on the mulm that gets deposited.
If you really feel you must clean the substrate (say its been several years or
it is really, really mucky and/or root-bound) then you probably should take
plants out and replant them one small area at a time. (Crypts won't like this
too much..) Once you have cleared an area, vaccume away the junk with your
python.

-Bruce Geist