If you know which line you want to delete, you can call
ax.lines.remove(line) where line is a line instance.
In [1]: line1, = plot(rand(10), 'ro')
In [2]: line2, = plot(rand(20), 'b--s')
In [3]: ax = gca()
In [4]: ax.lines.remove(line1)
In [5]: draw()
If you haven't saved the line instance, but can otherwise identify it
(eg you know it was the first line you plotted), you can do something
like
ax.lines.remove(ax.lines[0])
or if you have labeled the line, you can identify and remove it with
plot(x,y,label='my line')
line = [line for line in ax.lines if line.get_label()=='my line'][0]
ax.lines.remove(line)
JDH