Nanocrystalline carbon (n-C) thin films were deposited on Mo substrates using methane (CH4) and hydrogen (H2) by the hot-filament chemical vapor deposition (HFCVD) technique. Process parameters relevant to the secondary nucleation rate were systematically varied (0.3–2.0% methane concentrations, 700–900 °C deposition temperatures, and continuous forward and reverse bias during growth) to study the corresponding variations in film microstructure. Standard nondestructive complementary characterization tools such as scanning electron microscopy, x-ray diffraction, atomic force microscopy, Raman spectroscopy, and x-ray photoelectron spectroscopy were utilized to obtain a coherent and comprehensive picture of the microstructure of these films. Through these studies we obtained an integral picture of the material grown and learned how to control key material properties such as surface morphology (faceted versus evenly smooth), grain size (microcrystalline versus nanocrystalline), surface roughness (from rough 150 rms to smooth 70 rms), and bonding configuration (sp3 C versus sp2 C), which result in physical properties relevant for several technological applications. These findings also indicate that there exist fundamental differences between HFCVD and microwave CVD (MWCVD) for methane concentrations above 1%, whereas some similarities are drawn among films grown by ion-beam assisted deposition, HFCVD assisted by low-energy particle bombardment, and MWCVD using noble gas in replacement of traditionally used hydrogen.