The Bitmap class is having a method named MakeTransparent which takes the color as argument.
Example: Create a new windows form application and keep two PictureBox control on it. Set the image of PictureBox1 to the following image:
// Here the color at pixel 1, 1 is made as transparent
Bitmap bitmap = new Bitmap(pictureBox1.Image);
pictureBox2.Image = bitmap;
On invoking the above code you can see: