This may help:
images = LoadPixmapPNG("images.png") xsize = PixmapWidth(images) ysize = PixmapHeight(images) images_alpha = LoadPixmapPNG("images_alpha.png") new_images = CreatePixmap(xsize, ysize, PF_RGBA8888) For y = 0 Until ysize For x = 0 Until xsize WritePixel new_images, x, y, (ReadPixel(images, x, y) & $FFFFFF) | ((ReadPixel(images_alpha, x, y) & $FF) Shl 24) Next Next SavePixmapPNG new_images, "new_images.png", 9 DebugLog "Done!"