Numerous sky background subtraction techniques have been developed, since the first implementations of computer-based reduction of spectra. Kurtz and Mink (2000) for the first time discussed a PCA-based method which allowed them to subtract night sky background from multi-fiber spectroscopic observations without any additional sky observations. We hereby take this approach one step further with usage of NNMF instead of PCA and generalize it to long-slit and IFU spectra. This allows us to generate approximately 10 times as many valid eigenspectra because of non-negativity. We combine this approach with the algorithm proposed in Kelson (2003) to generate an oversampled sky model. We apply our method to “short”-slit spectra of low-mass galaxies originating from intermediate-resolution Echelle spectrographs (ESI at Keck, MagE at Magellan, X-Shooter at the VLT) when galaxies fill the entire slit and demonstrate its efficiency even when no offset sky observations were obtained.