Reproduce:

import pandas as pd
import numpy as np
from scipy import fftpack

x = np.array([1.,2.,3.,4.,5.])
xs = pd.Series(x)

print x
tmp = fftpack.rfft(x)
print x

print x
tmp = fftpack.rfft(xs)
print x

"""
output:
[ 1.  2.  3.  4.  5.]
[ 1.  2.  3.  4.  5.]
[ 1.  2.  3.  4.  5.]
[ 15.          -2.5          3.4409548   -2.5          0.81229924]
"""

posted also in scipy.github: https://github.com/scipy/scipy/issues/5790

Comment From: jreback

I would say this is a scipy issue. Series is essentially a duck-like ndarray, so I don't see why it should inplace modify it.