how to clip pandas dataframe column-wise?

Instead of a numpy array, you can use a Series so the labels are aligned:

df
Out: 
   A  B
0  1  4
1  2  5
2  3  6

df.clip(lower=pd.Series({'A': 2.5, 'B': 4.5}), axis=1)
Out: 
     A    B
0  2.5  4.5
1  2.5  5.0
2  3.0  6.0