MATLAB - Delete elements of binary files without loading entire file

There is no ftruncate() in Matlab, but you've got access to the full Java standard library in the JVM embedded in Matlab, and can use java.io.RandomAccessFile or the Java NIO classes to truncate a file. Here's a Matlab function that calls to Java to lop the last n bytes off a file. Should have minimal I/O cost. function remove_last_n_bytes_from_file(file, n) jFile = java.io.RandomAccessFile(file, 'rw'); currentLength = jFile.length(); wantLength = currentLength - n; fprintf('Truncating file %s: Resizing to %d to remove %d bytes\n', file, wantLength, n); jFile.setLength(wantLength); jFile.close(); You could also do it as a one-liner. java.io.RandomAccessFile('/path/to/my/file.bin', 'rw').setLength(n);

Since you don't want to read the file into MATLAB (understandably), you are dealing with system level commands. MATLAB has a facility to call system commands using the "system" command http://www.mathworks.com/access/helpdesk/help/techdoc/ref/system.html So now your problem is reduced to finding the shell command in your OS that will do it for you. Or you can write a program using truncate() (unix -- KennyTM) or SetEndOfFile (windows)

I don't know if MATLAB supports this, but see http://www.opengroup.org/onlinepubs/007908799/xsh/ftruncate.html.