Use os.walk to iterate recursively over directory content:
import os
root_dir = '.'
for directory, subdirectories, files in os.walk(root_dir):
for file in files:
print os.path.join(directory, file)
No real difference between os.system and subprocess.call here - unless you have to deal with strangely named files (filenames including spaces, quotation marks and so on). If this is the case, subprocess.call is definitely better, because you don't need to do any shell-quoting on file names. os.system is better when you need to accept any valid shell command, e.g. received from user in the configuration file.