Solution 1:

Let's try using a Counter here:

  1. Split sentences into words
  2. Compute global word frequency
  3. Filter words based on computed frequencies
  4. Join and re-assign

from collections import Counter
from itertools import chain

# split words into lists
v = df['Col2'].str.split().tolist() # [s.split() for s in df['Col2'].tolist()]
# compute global word frequency
c = Counter(chain.from_iterable(v))
# filter, join, and re-assign
df['Col2'] = [' '.join([j for j in i if c[j] > 1]) for i in v]

df
   Col1                Col2
0     1  how to remove word
1     5  how to remove word

Solution 2:

Method from get_dummies

s=df.set_index('Col1').Col2.str.get_dummies(sep=' ')


s.loc[:,s.all()].stack().reset_index(level=1).groupby('Col1')['level_1'].apply(' '.join).reset_index(name='Col2')
Out[155]: 
   Col1                Col2
0     1  how remove to word
1     5  how remove to word