will my page set up effect SEO?

[mfahey]

I hired a programmer to build my site.

When he installed on the servers, the page names come up like...

company.com/company

company.com/company/schools.php
company.com/company/register.php

etc

I asked him to remove the duplicate names..he said he created folder and loaded and it would be difficult to change...

Is there an issue here with seo or even site maps?