An atomic force microscope (AFM) has been used to reveal residual sub-micron sized decomposition sites in drop weight impacted RDX and laser irradiated AP crystals. In impacted RDX, the small and early reaction sites observed are hemispherical craters, ranging in size from 20–300 nm. The smallest reaction site encompassed about 10,000 molecules with an expected energy evolution of 2 × 10−14 J. On a somewhat larger scale hillocks of 200–800 nm were observed, their shape giving evidence of internal reaction and hot spot melting. Dislocation densities as high as 5 × 1012 per cm2 were observed in sub-ignited RDX. High resolution AFM images of the RDX lattice structure indicate molecular rotation as well as displacements at dislocation sites. In AP, after nanosecond pulsed laser irradiation, reaction sites were trumpet shaped with a smallest size of approximately 50 nm. Most sites contained a crystallographically oriented central square lid formed above the surrounding crystal surface, probably relating to the orthorhombic to cubic phase transition documented in micron scale cracking patterns observed at the laser heated sites.