Remove the extra plot in the matplotlib subplot

Try this:

fig.delaxes(axes[1][2])

A much more flexible way to create subplots is the fig.add_axes() method. The parameters is a list of rect coordinates: fig.add_axes([x, y, xsize, ysize]). The values are relative to the canvas size, so an xsize of 0.5 means the subplot has half the width of the window.