Black velvet would really be the ultimate for providing a totally black
background, but I just use a black paper "tent" or black paper box to cover
the shell.  As Tom said, for darker shells a lighter background is
preferable.  Shadows on the background can be avoided by keeping the
background well above the shell.  About 6 to 8 inches height works well for
me.  When you lay a shell on the glass, it tends to assume its own preferred
position, usually with the spire tilted down toward the glass, or sometimes
the anterior end.  Smooth round shells like cowries, olives and moon snails
roll into odd positions, and worse, they sometimes rotate on the glass during
scanning, from the vibrations of the scanner.  I use a variety of methods to
hold the shell in place so that I can get a straight-on view, and make sure
the shell doesn't move.  Like Tom, I use the computer (Photoshop software)
afterwards, to remove anything in the background that I don't want there, so
when I'm scanning I concentrate fully on what the shell will look like, not
the background.  Therefore I may lay the edge of a book on top of the shell
to hold it in position.  But my usual method involves a couple of lumps of
clay and a pencil.  A big lump of modeling clay serves as a base, off to the
side.  The pencil sticks out of the clay, and extends out over the glass of
the scanner, and on the other end of the pencil I stick a small blob of clay.
 I stick the small blob lightly to the upper surface of the shell.  Then I
can position the shell at any angle, and it stays in that position while it
is scanned.  For example, I lift the anterior end of a cone off the glass, so
that the central axis of the shell is parallel to the glass.  Once it is in
position, I put the paper tent over the whole works, and scan it.
Regards,
Paul M.