The way I have removed them is simply JOIN another piece of geometry to them.
For solids join another solid to it. I use a small cylinder and if I don't want it to show up outside of the solid (a sphere in this case) I hide it within the solid as shown in the image below.
For surfaces, I just use a small void cylinder and "cut" the surface with the void. I don't use a solid cylinder (as the case with the sphere) because solids do not join with surfaces as shown in the image below.
NOTE: When you "cut" a surface with a void or "join" a solid with another solid then you are essentially creating a "new" element that is similar to a Boolean operation in 3dsmax. This new element has no seams! Hope this helps.