Surface-assisted laser desorption ionization (SALDI) is an approach for gas-phase ion generation for mass spectrometry using laser excitation on typically conductive or semiconductive nanostructures. Here, we introduce insulator nanostructure desorption ionization mass spectrometry (INDI-MS), a nanostructured polymer substrate for SALDI-MS analysis of small molecules and peptides. INDI-MS surfaces are produced through the self-assembly of a perfluoroalkyl silsesquioxane nanostructures in a single chemical vapor deposition silanization-step. We find that surfaces formed from the perfluorooctyltrichlorosilane monomer assemble semielliptical features with a 10 nm height, diameters between 10 and 50 nm, and have attomole-femtomole sensitivities for selected analytes. Surfaces prepared with silanes that either lack the trichloro or perfluoro groups, lack sensitivity. Further, we demonstrate that hydrophobic INDI regions can be micropatterned onto hydrophilic surfaces to perform on-chip self-desalting in an array format.