acf-file-custom.php

<?php

class ACF_File_Custom {

	private static $instance;
	public static function register() {
		if ( self::$instance == null ) {
			self::$instance = new ACF_File_Custom();
		}
	}	
	
	private $_fields = array();
	
	private function __construct() {
		
		/* Change the field key here.  
		 * You can change the subdirectory to whatever you want as well. 
		 * This code currently will place the files in the default uploads directory + whatever you configure here.
		 * So this example will result in files being in wp-content/uploads/secure/filename.ext 
		*/
		
		$this->_fields['field_56b60ed95cb71'] = '/secure';  //Change the directory to whatever you want.  
		
		//$this->_fields['another_field_key'] = '/another-secure-directory';
		
		add_filter( 'upload_dir', array($this, 'change_upload_dir') );
	}

	public function change_upload_dir( $dir ) {
		if (isset($_POST['_acfuploader']) && !empty($_POST['_acfuploader'])){
			$key = $_POST['_acfuploader'];
			if (array_key_exists($key, $this->_fields)){
				
				/*
				 * The default $dir is as follows. 
				[path] => (string) /Applications/XAMPP/xamppfiles/htdocs/local.wordpress.edu/wp-content/uploads/2016/02
				[url] => (string) http://local.wordpress.com/wp-content/uploads/2016/02
				[subdir] => (string) /2016/02
				[basedir] => (string) /Applications/XAMPP/xamppfiles/htdocs/local.wordpress.edu/wp-content/uploads
				[baseurl] => (string) http://local.wordpress.com/wp-content/uploads
				[error] => (bool) false
				 */
				
				$destination_folder_url = $this->_fields[$key];
				$dir['basedir'] = $dir['basedir'] . $destination_folder_url;
				$dir['baseurl'] = $dir['baseurl'] . $destination_folder_url;
				$dir['subdir'] = $destination_folder_url;
				$dir['url'] = $dir['baseurl'] . $destination_folder_url;
				
				$dir['path'] = $dir['basedir'];
			}
			
		}
		
		return $dir;
	}
}
ACF_File_Custom::register();