CodeIgniter is a framework based on MVC principles. As a result, you would usually separate application logic, data abstraction and "output" into their respective areas for CodeIgniter use. In this case: controllers, models and views.
Just for reference, you should usually have you "data" code as a model function, in this case the get_where functionality. I highly suggest you read through the provided User Guide to get to grips with CodeIgniter, it should hold your hand through most steps.
function files(){
$owner = $this->auth->get_user();
$data['files'] = $this->db->get_where('files', array('owner =' => '$owner'))->result();
$this->load->view('name_of_my_view', $data);
}
And then make sure to use the correct variable in your view:
<?php foreach($files as $row): ?>
<span><?=$row['name']; ?></span>
<?php endforeach; ?>
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