>I have eps files but their margin are too big

You could use ps2eps program. As far as I understand, that
computes the bounding box of a postscript file by actually
rasterizing it and checking where the image ends. 

You could convert your EPS file to postscript, for example
by inserting it into a LyX document and exporting it as
postscript, or maybe ps2eps can handle directly also EPS files.

This isn't specifically easy solution though (needs some
work at the command line level), so read first if others give you easier
tricks.

http://www.ee.oulu.fi/~tuukkat/tmp/ps2eps.tar.gz

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