MeV SIMS is a type of secondary ion mass spectrometry (SIMS) technique where molecules are desorbed from the sample surface with ions of MeV energies. In this work, we present a novel system for molecular imaging of organic materials using a continuous analytical beam and a start trigger for timing based on the detection of secondary electrons. The sample is imaged by a collimated primary ion beam and scanning of the target with a lateral resolution of ∼20 μm. The mass of the analyzed molecules is determined with a reflectron-type time-of-flight (TOF) analyzer, where the START signal for the TOF measurement is generated by the secondary electrons emitted from a thin carbon foil (∼5 nm) placed over the beam collimator. With this new configuration of the MeV SIMS setup, a primary ion beam with the highest possible electronic stopping can be used (i.e., highest secondary molecular yield), and samples of any thickness can be analyzed. Since the electrons are collected from the thin foil rather than from the sample surface, the detection efficiency of secondary electrons is always the same for any type of analyzed material. Due to the ability to scan the samples by a piezo stage, samples of a few cm in surface size can be imaged. The imaging capabilities of MeV SIMS are demonstrated on crossing ink lines deposited on paper, a thin section of a mouse brain, and a fingerprint deposited on a thick Si wafer to show the potential application of the presented technique for analytical purposes in biology and forensic science.