AFAIK the only way to avoid caching a file is to use O_DIRECT to begin with.
You can use dd with iflag=direct to read a file with O_DIRECT and pass it to any utility that can read from stdin.
FADV_DONTNEED doesn't actually flush files from the Linux pagecache.

# dd if=massivefile of=/dev/null bs=2M  
# fadv <massivefile

where fadv.c is:

#include <fcntl.h>
#include <sys/types.h>
#include <unistd.h>

int main(int argc, char **argv)
{ posix_fadvise(0, 0, lseek(0, SEEK_END, 0), POSIX_FADV_DONTNEED);
  return 0;
}

But memory wasn't freed (large file is >10GB large)

# free  
             total       used       free     shared    buffers     cached  
Mem:       8108404    7953940     154464     402172          0    5910868  
-/+ buffers/cache:    2043072    6065332  
Swap:      1048568          0    1048568

The only way to prevent a file from being cached is to use O_DIRECT. dd is your friend.
If you don't want to use O_DIRECT, notice that the damage might be done already afterwards (other more important things might be discarded from the cache).

# fgrep MemFree: /proc/meminfo
4691788 KB
# dd if=massivefile of=/dev/null bs=2M  
# fadv <massivefile
# fgrep MemFree: /proc/meminfo
5097264 KB

where fadv.c is (use stdin to make the code ultra simple):

#include <fcntl.h>
#include <sys/types.h>
#include <unistd.h>

int main(int argc, char **argv)
{ posix_fadvise(0, 0, lseek(0, 0, SEEK_END), POSIX_FADV_DONTNEED);
  return 0;
}

Notice that afterwards there is more free memory than before, meaning data that was in the cache before was thrown out. However if you read the file with O_DIRECT:

  # fgrep MemFree: /proc/meminfo
  MemFree:         5091464 kB
  # dd if=verylargefile bs=2M of=/dev/null iflag=direct
  6141+1 records in
  6141+1 records out
  12880669515 bytes (13 GB) copied, 72,7641 s, 177 MB/s
  # fgrep MemFree: /proc/meminfo
  MemFree:         5074164 kB

Now there's a little less memory free, meaning other activity used up some memory, but the actual read of this 13GB file didn't wash the cache.