We report on a simple method of inducing self-insulation of the thin-film transistors via manipulation of the chemical interactions between the organic molecules and the surfaces where they are deposited. We use pentafluorobenzenethiol (PFBT) treatment of the contacts and investigate the thin film formation of different types of chemical compounds. In particular, three similar organic molecules: triisopropyl-silylethynyl pentacene (TIPS pentacene), triisopropyl-silylethynyl peri-fluoro-pentacene (TIPS PFP) and triisopropyl-silylethynyl cata-fluoro-pentacene (TIPS CFP), were studied and compared to better understand how the molecular, crystal structure and thin film formation influence the electrical behavior of devices fabricated with them. The molecules exhibit significantly different interactions with the chemically treated substrates. The field-effect mobilities of these devices are directly related to their thin film microstructure.