Strong field ionization (SFI) was applied for the secondary neutral mass spectrometry (SNMS) of patterned rubrene films, mouse brain sections, and Botryococcus braunii algal cell colonies. Molecular ions of rubrene, cholesterol, C31 diene/triene, and three wax monoesters were detected, representing some of the largest organic molecules ever ionized intact by a laser post-ionization experiment. In rubrene, the SFI SNMS molecular ion signal was ~4 times higher than in the corresponding secondary-ion mass spectroscopy (SIMS) analysis. In the biological samples, the achieved signal improvements varied among molecules and sampling locations, with SFI SNMS, in some cases, revealing analytes made completely undetectable by the influence of matrix effects in SIMS.