Cut holes in sprite using other sprites

If you don't want to write a shader you can use the system drawing library: https://msdn.microsoft.com/en-us/library/system.drawing.bitmap(v=vs.110).aspx

With this you can create a Bitmap that contains all your pixels. Then you can just get the bounds of your textures and remove with SetPixel();

 //You can convert a png or a jpg to a bitmap. 
 string path = "./path/to/your_image.bmp";
 Bitmap img = (Bitmap)Bitmap.FromFile(path);

 //Some loop to get the bounds of your sprite lets say its one pixel
 int x = 0;
 int y = 0;
 Color color = Color.White;
 
 img.SetPixel(x, y, color);
 img.Save(path);

This is an old question, but for those still looking, it can be solved using Unity's Sprite Mask component. To set this up, all you need is to set the "mask interaction" option to "visible outside mask" on the main sprite and then make sprite masks with the others.