POSIX does not include a sensible way to list or close a range of file descriptors.
So we have to loop over the full range (like from 3 to 1023), closing the file descriptors one at a time.
Or, if we have a /proc file system, we can read the list of open file descriptors in /proc/self/fd and close just those.  This can be quicker than closing all possible file descriptors.
import os
def close_files(fd_min=3, fd_max=-1):
    if os.path.exists('/proc/self/fd'):
        close_files_with_procfs(fd_min, fd_max)
    else:
        close_files_exhaustively(fd_min, fd_max)
def close_files_exhaustively(fd_min=3, fd_max=-1):
    import resource
    fd_top = resource.getrlimit(resource.RLIMIT_NOFILE)[1] - 1
    if fd_max == -1 or fd_max > fd_top:
        fd_max = fd_top
    for fd in range(fd_min, fd_max+1):
        try:
            os.close(fd)
        except OSError:
            pass
def close_files_with_procfs(fd_min=3, fd_max=-1):
    for nm in os.listdir("/proc/self/fd"):
        if nm.startswith('.'):
            continue
        fd = int(nm)
        if fd >= fd_min and (fd_max == -1 or fd < fd_max):
            try:
                os.close(fd)
            except OSError:
                pass
def timereps(reps, func):
    from time import time
    start = time()
    for i in range(0, reps):
        func()
    end = time()
    return (end - start) / reps
print "close_files: %f" % timereps(100, lambda: close_files())
print "close_files_exhaustively: %f" % timereps(100, lambda: close_files_exhaustively())
print "close_files_with_procfs: %f" % timereps(1000, lambda: close_files_with_procfs())
On my system:
$ python ./close_fds.py 
close_files: 0.000094
close_files_exhaustively: 0.010151
close_files_with_procfs: 0.000039