This work continues the studies of low-threshold field electron emission from thin (6 – 10 nm) films of refractory metals (Mo or Zr) deposited on flat Si substrates. Now, we have investigated the changes in the films’ morphology induced by thermo- and electroforming procedures and by the extraction of emission current. In SEM images of the samples taken after emission experiments, we observed the signs of solid-state dewetting (agglomeration) of the films, presumably caused by ion bombardment. This hypothesis was verified by SRIM simulations of the effect of ions on Mo-film/Si-substrate structure, as well as by an experiment at a HVEE-500 ion implanter.