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You can save the search formats:"=EPUB" and use the Calibre Content Server's sorted By Searches option to see just the books with ePub format. When using a web-browser the mobile interface for the content server shows the download formats immediately but doesn't give the option of using saved searches while the non-mobile interface shows the formats in the details section and also gives the option of sorting by saved searches.
I tend to use virtual libraries for library repair and maintenance work simply to avoid the need to add books back to my Main library once I've fixed things up. (I don't mind having a number of virtual libraries with different functions)
So if I wished to split my library by format I'd set up three searches as follows and save them both as searches and as virtual libraries.
(1) formats:"=EPUB" or formats:"=MOBI"
(2) formats:"=PDF"
(3) not formats:"=EPUB" and not formats:"=MOBI" and not formats:"=PDF"
If you really want separate libraries then setting up an appropriate search, selecting all the books, right clicking, selecting Save to Disk (single format), importing those books to the desired library and then removing the undesired format(s) from your orginal library would work although likely with a loss of metadata.
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