MASSKIP reduces, calibrates, and performs photometric analysis on images acquired with Multi-Amplifier Sensing (MAS) Skipper CCDs. It handles amplifier heterogeneity and deep sub-electron read noise regimes. The Python pipeline supports Multi-Extension FITS (MEF) files, executing overscan correction per extension with independent ROI shifting, pixel-by-pixel bias subtraction, and normalized master flat creation. It applies variance-weighted and signal-to-noise ratio-weighted combination methods to dynamically suppress noisy amplifiers and achieve theoretical sub-electron read noise limits. MASSKIP also includes enhanced cosmic ray rejection, dynamic WCS injection, and a built-in photometry module utilizing photutils.