Вы, вероятно, ищете zorder:
from pylab import *
fig = figure(1)
fig.clf()
ax = subplot(111)
rect = matplotlib.patches.Rectangle((0.2,0.2), 0.3, 0.3, fc = '0.5', ec = '0.0')
ax.add_patch(rect)
ax.text(.4, .4, "Help me, there is a rectangle stuck under me!")
fig = figure(2)
fig.clf()
ax = subplot(111)
rect = matplotlib.patches.Rectangle((0.2,0.2), 0.3, 0.3, fc = '0.5', ec = '0.0')
ax.add_patch(rect)
ax.text(.4, .4, "Help me, I'm stuck under a rectangle!", zorder = -1)
show()