The interaction of Mn thin films on atomically flat GaN(000 over(1, ̄)) has been investigated by Scanning Tunneling Microscopy (STM) and Time of Flight Secondary Ion Mass Spectroscopy (ToF-SIMS). GaN surfaces prepared by repeated sputtering/annealing cycles show various reconstructions but essentially the 6×6 one. A high density of small islands (height 0.6 nm, diameter 5 nm) nucleates upon deposition of 0.3 ML Mn. Upon annealing at 575 C, these islands coalesce into larger islands (height 4 nm, diameter 50 nm) between which the GaN surface is visible. Atomically resolved STM images between the islands show the (3×3) reconstruction of GaN. Annealing the sample further to 675 C leads to the restoration of a bare GaN surface. ToF-SIMS reveals that Mn diffused into the bulk of the sample.