Is it possible to make one side of a cylinder square while leaving the other alone? If so how would I go about it? I have a tree branch that I need to connect to a trunk. The number of edges on the cylindrical branch will not connect up with the square hole on my trunk...Any ideas?
Don't know if this is what you wanted, but you may just bridge the vertices between square and circle to create this kind of shape. Add a plane and subdivide it as many times as you want. Then add a circle with the number of vertices matching the number of the vertices on the edges of the square/plane. Finally select them as pictured below, press Spacebar and type Bridge-->Bridge Edge Loops.
NOTE: There is similar answer about this here on BSE, but I can't find it.
To understand a little bit more of how this works in depth have a look at this post
The trick is to set your pivot mode to Active Element.
Then, select everything you would like to square off, making sure that your last element selected is the location you want your dquare edge to end up (In my case I wanted to square it off in the '-Y' Axis at the bottom edge of this cylinder).
Then, S >> Numpad 0 >> Enter.