Electron microscopy (EM) techniques are used to investigate the microstructure of ultrathin carbon layers obtained by focused ion beam induced deposition (FIBID). The investigation determines the crystalline structure, chemical bonding and elemental contents of FIBID-C materials. The effect of a thermal treatment to the ultrathin C films is analyzed. As-deposited FIBID-C is a metastable material transforming at mid-high temperatures. Evidence of its graphitization by metal catalysis is presented. Understanding of the heat transformation and crystallization is established based on the observations. Specifically, carbonization, H desorption decomposition, and graphitization, driven by high temperature metal-induced crystallization, are the identified processes. Demonstration of the graphitization of ultrathin FIBID-C enables a strategy towards graphene integrative planar technologies.