import numpy as np
filenames = ["foo", "bar"]
col1_all = 0  #data will be stored in these 3 arrays
col2_all = 0
col3_all = 0
for f in filename:
    col1, col2, col3 = np.loadtxt(f, unpack=True)
    if col1.shape[0] > 0: # I can't guarantee file won't be empty
        if type(col1_all) == int:
            # if there is no data read in yet, just copy arrays
            col1_all = col1[:]
            col2_all = col2[:]
            col3_all = col3[:]
        else:
            col1_all = np.concatenate((col1_all, col1))
            col2_all = np.concatenate((col2_all, col2))
            col3_all = np.concatenate((col3_all, col3))