  We study the thermal fluctuations of vortex positions in small vortex
clusters in a harmonically trapped rotating Bose-Einstein condensate. It is
shown that the order-disorder transition of two-shells clusters occurs via the
decoupling of shells with respect to each other. The corresponding "melting"
temperature depends stronly on the commensurability between numbers of vortices
in shells. We show that "melting" can be achieved at experimentally attainable
parameters and very low temperatures. Also studied is the effect of thermal
fluctuations on vortices in an anisotropic trap with small quadrupole
deformation. We show that thermal fluctuations lead to the decoupling of a
vortex cluster from the pinning potential produced by this deformation. The
decoupling temperatures are estimated and strong commensurability effects are
revealed.
