You would end up with broken links if you simply copied the files over to a new folder.
What you would need to do to avoid this is install a plugin like WP Migrate DB and enter in the new server path.
You would then need to create another database taking note of the name, username and password which you would need to change in the wp-config.php file of the new installation.
If its a new site without any content or customization, you would be better off to simply install a new version of WorPress in a new folder on your server.
Here’s the way to install WordPress manually. http://codex.wordpress.org/Installing_WordPress
There are also plugins like duplicator which maybe useful to you.
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