Retaining sub-sites on moving to WP

Hi,

I would like to update my website to a wordpress site. I have built the wp site in its own sub-directory and intend in due course to move it to the root.

My question: my old site has several directories that are, in effect, mini sites in their own right. They are not wp sites. I have linked to them from my wp pages. Will I be able to retain these directories as they are on the root server alongside the wp?

Thanks
Andrew