Secondary ion mass spectrometry (SIMS) applied in the event-by-event bombardment/detection mode is uniquely suited for the characterization of individual nano-objects. In this approach, nano-objects are examined one-by-one, allowing for the detection of variations in composition. The validity of the analysis depends upon the ability to physically isolate the nano-objects on a chemically inert support. This requirement can be realized by deposition of the nano-objects on a Nano-Assisted Laser Desorption/Ionization (NALDI™) plate. The featured nanostructured surface provides a support where nano-objects can be isolated if the deposition is performed at a proper concentration. We demonstrate the characterization of individual nano-objects on a NALDI™ plate for two different types of nanometric bacteriophages: Qβ and M13. Scanning electron microscope (SEM) images verified that the integrity of the phages is preserved on the NALDI™ substrate. Mass spectrometric data show secondary ions from the phages are identified and resolved from those from the underlying substrate.