Why isn't there any audio when I convert my videos?

I downloaded videos that are formatted as MKV files...but whenever I try and convert them to MP4 (for my iPod), there is no audio...how can I convert my video WITH audio if it's an MKV with AAC audio? Does anyone know of a site that can convert MKV with AAC to MP4? I would like it if it was freeware...please share any sites that may help me with this problem please? D: Thank you guys :)