iBooks use a format called ePub. There are a lot utilities out there that can do this conversion for you, but the best one I found was Calibre.
Calibre is a free and open source e-book library management application developed by users of e-books for users of e-books. If you have many PDF files or some other format ebooks you want to put on iPad, there is a free converter called calibre. Calibre enables you to manage your entire eBooks collection (rate, tag, sort, download metadata and covers etc.) and it accepts a wide range of formats for conversion. Calibre runs on Windows, Mac OS X AND Linux.
Now that we’ve introduced the software, let’s get down to business
Here are the Steps which will convert you PDF and ebook into ibook (epub format )
Step1. Download and install calibre ebook converter. The interface is very slightly different in each version. These tutorial images are captured on Mac, but Windows users should have no problem at all following along.
Step2. Find the PDF file you want to convert.
Step3. The first time you run calibre it will take you through a quick setup. The first thing you’ll want to do is specify your ‘ebooks’ folder. This is the location you’ll save your .ePub files.
Step4. After you set the ebooks folder, click continue Then select Apple from the Manufacturers list, and iPhone/iTouch + Stanza from the Devices list.
Step5. Click ‘continue’, then you will see the main calibre interface. Click the Add books button in the top-left corner of the window to import your PDF file into calibre.
Step6. Now click the small ‘arrow’ next to the Edit Meta information and select Download metadata and cover files. Calibre will now download additional information about your PDF/ebook – if it can find it. If it’s an eBook (as a .pdf), you may need to manually enter the book title and author name if it isn’t present when you load it into calibre initially.
Step7. After finish download the ebook meta information. Click the small arrow next to the Convert E-books button. From the list that will appear, select Convert individually. You will be prompted with a ‘summary’ window prior to calibre making the final conversion. Click the OK button.
Step8. After the conversion is finished, you can locate the folder on step3 where you save the ePub file. Then connect your iPad to your Mac or PC, and launch iTunes. From the iTunes menu select File -> Add to Library… to import the converted ePub file. The new .ePub file will now appear in the Books section of iTunes.
Step9. Select your iPad in iTunes and select the Books tab. After confirming your new .ePub book is listed, click the Sync button.