I recieve page not found error after i attempt to run my php file running around the root folder of my apache. Other php files run fine(anyway this can be a magento based site). Could it be because i moved the file through FTP? Can a server be set up to not run some specific files? How do i get round this? has is got something related to .htacess?

Make sure to submitted your file in to the /www or /httpdocs subdirectory. If that's the case, look into the permissions of the file.

Does the fiel have a similar extension because the other php files that actually work.

ie. myfile.php or myfile.php4

The default config for apache identifies that php files possess the extension "php4" as php version 3. and before aren't suitable for the present versions. Usually plain "php" extension is re-enabled but not inside your situation.