Yes but you will need to have Phalcon driving behind the scenes so to speak. Traditionally one doesn't do this since it is more work than one would expect. Changing to an MVC framework should be done in one move.
However to answer your question:
You need to set a phalcon project. In your routes you need to add something like this:
$router->add('thing.php', ['controller' => 'onlyphp' , 'action' => 'index'])
$router->add('thing2.php', ['controller' => 'onlyphp' , 'action' => 'index'])
which will instruct phalcon to process thing.php with the thing controller. In that controller you can have code that will read thing.php and send it to the view.
Slowly you can move each of the php files to their respective controllers.and thus removing the old functionality.