You can implement transparency when doing any of the following:
Once a region is defined, you can create a mask from it, using the CreateMaskFromRegion method, which you can save in the alpha channel of a 16- or 32-bit file. Refer to the SetAlphaImage method for an example of how to save a region in an alpha channel.
When specifying a transparent color, you can use the Windows PALETTEINDEX macro to refer to a particular palette index (where the RasterColor value is >= 0x01000000). Using a palette index for transparency means that one of the remaining colors in the palette can have the same RGB value as the transparent color, without being interpreted as transparent.