I am not a lapidarist, so maybe someone else can give you better advice.
My guess is that your beads were "polished" by laquering them. If so, you could clean residual laquer off by washing them in laquer thinner and then reapply a clear spray laquer. Not the best way to go.
If the beads are spheres, not random shapes, you could remove the string, polish each bead by hand and then restring them. Malachite is soft, and polishing by hand would not be difficult. You could use automotive rubbing compound on a soft cloth. Then wash the residue off with paint thinner.
From Don Peck - July 16, 2007 at 10:16:26