I guess it depends when you want these files to be converted. For instance if these files are to be converted at runtime, then you will want to look into custom pipelines. For instance, BizTalk can receive a flat file(csv or fixed width), as this message is received, it is "disassembled" into an xml file in the receive pipeline. So by the time the file gets to your Orchestration it is in XML format.
There is a design time component called the Flat File schema wizard(which showed up in 2006) that helps you define the structure of the flat file and how it will look in XML. The end result is that you will have a Flat File schema which you will use in your custom pipeline.
There is also a 3rd party component, called FarPoint i believe, that allows you to perform a similar function, but with Excel files. I have not used it so I can't say how well/poorly it functions.
Hope this helps…