How to calculate/edit alpha channel(white area)of given texture at runtime

(in my case i need to calculate/edit alpha value of a manikin top mesh).What i am trying to do is i have set of garment blocks with me and once i change those blocks area it will automatically change the 3d mesh accordingly).
Currently I am selecting Transparent/Cutout/diffuse as a shader for 3D(mesh)Top And what i have done is edit alpha channel(white area into black) of the material texture of the given mesh using Photoshop.By doing so i can change the length,width on that material texture and it will automatically disable the
3D mesh according to that material texture editing.I need to do it Programatically in unity run time. I know this is kind a difficult task to do for mid level dev like me.So please feel free to give me solution.