Infrared molecular beam depletion spectroscopy of small methanol and acetonitrile clusters embedded in large helium clusters has been studied in the spectral region of the CO stretch and the CH3 rock mode from 1023 to 1059 cm(-1). The results are compared with the experimental spectra of the corresponding free clusters generated in adiabatic expansions and calculations based on density functional theory or empirical potential models. For methanol clusters, the two types of experimental results are the same for the dimer and trimer structure. Different isomers are found in cold helium for the tetramer and pentamer, namely a monomer and dimer attached to a cyclic trimer. For acetonitrile clusters in helium, aside from the dimer, different structures are observed. The spectra from the trimer to the hexamer are dominated by structures which contain the antiparallel dimer as building block with D-2d symmetry for the tetramer. They do not correspond to the minimum configurations observed for the free clusters. The fragmentation of the two cluster groups in helium droplets by electron impact ionization is discussed.