<?php
class Test
{
public function index( )
{
    $arr = array( 
        array('a' => 'aap', 'n' => 'noot', 'm' => 'mies'), 
        array('a' => 'ding', 'b' => 'flof', 'c' => 'bips'), 
        array( 'd' => 'do', 'e' => 're', 'c' => 'mi') 
    );

    $func = array( $this, '_user_func' );

    foreach ($arr as $key => &$value) {
        //$this->_do_callback($func, $value, $key); // No exception but array not modified afterwards
		$param = array(&$value);
        call_user_func( $func, $param, $key ); // Exception: Parameter 1 to TestRef::user_func() expected to be a reference, value given
    }
	unset($value);
    var_dump($arr);
}

private function _do_callback( $func, array &$row, $row_id )
{
    if ( is_callable( $func ) )
    {
        return call_user_func( $func, $row, $row_id );
    }
    else
    {
        throw new Exception( "Error doing callback. Callback empty or not a callable function." );
    }
}

private function _user_func( $_arr, $index )
{
	$arr = &$_arr[0];
    foreach ($arr as $key => $value) {
        $arr[$key] = 'replaced';
    }
    //var_dump($arr); // Works!
}
}

$test = new Test;

$test->index();