I have a sample PDF file with crop marks and bleed marks which i am looking for a solution where I can crop them.
The scripts I have tried Imagick, PDFkrop, Ghostscript ,PDFtk,TCPDF which does the job but missing one important thing. After cropping the pdf those software listed above removes the hyperlinks from text.
How can i crop a pdf and preserve the hyperlinks?
Ghostscript won't remove link annotations, though possibly that's not what you mean by hyperlinks.
As I've said on a number of oocasions, Ghostscript doesn't manipulate PDF files, but it can create a new PDF file with alterations.
You don't say what version of Ghostscript you are using, if its very old then you may simply be running up against a bug. The first thing to do is make sure you are using a recent version, ideally the current version. If you are still having problems, post the command line and a link to the PDF file.