As Idolse said, calibre converts PDFs to a more conventional ebook format. Not all forms of PDFs convert well and/or won't convert at all. All my PDF books and magazines are image only (the magazines are searchable PDFs) and I have no idea if they will convert or not since I never had the patience to wait on them.
If you have the file associations in your computer set to open PDFs in a non-calibre viewer, such as Adobe Reader, Foxit Reader, etc., just go into Preferences in calibre and, under Behavior, uncheck PDF form the Internal Viewer selections. Now, when you open a PDF book in calibre, it will open in the viewer your computer file association is set for. I use Adobe Acrobat Standard to read my PDFs.