This is one way to do it. Comments on the code in-line:
import csv
# List of your files
file_names = ['file1', 'file2']
# Output list of generator objects
o_data = []
# Open files in the succession and
# store the file_name as the first
# element followed by the elements of
# the third column.
for afile in file_names:
file_h = open(afile)
a_list = []
a_list.append(afile)
csv_reader = csv.reader(file_h, delimiter=' ')
for row in csv_reader:
a_list.append(row[2])
# Convert the list to a generator object
o_data.append((n for n in a_list))
file_h.close()
# Use zip and csv writer to iterate
# through the generator objects and
# write out to the output file
with open('output', 'w') as op_file:
csv_writer = csv.writer(op_file, delimiter=' ')
for row in list(zip(*o_data)):
csv_writer.writerow(row)
op_file.close()