A functionality of the novel black silicon based nanostructured surfaces (BS 2) with different metal surface modifications was tested by time-of-flight secondary ion mass spectrometry (TOF SIMS). Mainly two surface functions were studied: analytical signal enhancement and analyte pre-ionization effect in SIMS due to nanostructure type and the assistance of the noble metal surface coating (Ag or Au) for secondary ion formation. As a testing analyte a Rhodamine 6G was applied. Bi+ has been used as SIMS primary ions. It was found out that SIMS signal enhancement of the analyte significantly depends on Ag layer thickness and measured ion mode (negative, positive). The best SIMS signal enhancement was obtained at BS2 surface coated with 400 nm of Ag layer. SIMS fragmentation schemes were developed for a model analyte deposited onto a silver and gold surface. Significant differences in pre-ionization effects can play an important role in the SIMS analysis due to identification and spectra interpretation. (C) 2009 Elsevier B.V. All rights reserved.