I guess you are referring to SDL Analyse? At the moment the CSV report only returns a summary level, so you don't get the individual files. I also think it makes sense to do this so I will add it to the list of requirements we have for a future release of this tool.
In the meantime perhaps you'll find this application useful:
This little tool is very handy, although you do have to create a Project in Studio first. Once you have done this you can get your reports based on a summary per project based on language, or you can switch to the files view and get the details by file, so like this for example:
This can then be saved as CSV. Have a play anyway, it's very simple to use as you just select the files or the projects you need and then click on "Copy Word Counts" or right-click and select "Copy Word Counts" or use a keyboard shortcut. Any of these actions places the analysis on the windows clipboard and you can paste to Excel, to an email as a formatted html, or to notepad as a tab separated file.
That might be the easiest solution for you for now.