Thermal cleaning in ultrahigh vacuum of ZnO nanocrystals distributed on SiO2/Si surfaces has been studied using spectroscopic photoemission and low energy electron microscopy (SPELEEM). This study thus concern weakly bound ZnO nanocrystals covering only 5%-10% of the substrate. Chemical properties, crystallinity, and distribution of nanocrystals are used to correlate images acquired with the different techniques showing excellent correspondence. The nanocrystals are shown to be clean enough after thermal cleaning at 650 degrees C to be imaged by LEEM and x-ray PEEM as well as chemically analyzed by site selective x-ray photoelectron spectroscopy (mu-XPS). mu-XPS shows a sharp Zn 3d peak and resolve differences in O 1s states in oxides. The strong LEEM reflections together with the obtained chemical information indicates that the ZnO nanocrystals were thermally cleaned, but do not indicate any decomposition of the nanocrystals. mu-XPS was also used to determine the thickness of SiO2 on Si. This article is the first to our knowledge where the versatile technique SPELEEM has been used to characterize ZnO nanocrystals.