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Do you mean file format (e.g. epub, pdf etc) or are you asking about control of the filenames?
If you means filenames then calibre allows you to specify the filename masks to be used for the "Save to Disk" and "Send to Device" options.
One thing that is not currently available that has been requested is a feature to allow a mask for the name stored inside a book as part of its metadata. That would allow items like series name and number to be added to the name displayed by readers that take their values from the file metadata. I can see this coming as soon as someone gets enough motivation to implement the feature.
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