[willus]

Originally Posted by dgvirtual

I am having problem dealing with superscript (footnote references) in files.

Here is the original pdf, that has reference 60 in the second paragraph: https://dl.dropbox.com/u/4047484/superscript-input.pdf

And here is the output file with pretty much default options used: https://dl.dropbox.com/u/4047484/superscript-output.pdf

As you can see, the superscript causes two lines not to be treated as separate lines of text...

Is there a way to deal with this problem?

Yes--use a larger value for the -gtr option (default is 0.006). This worked with your particular example:

k2pdfopt -gtr 0.03 superscript-input.pdf

This makes k2pdfopt more aggressive about breaking apart lines of text, but potentially at the expense of inadvertently breaking apart figures. For more on options, see my help page with the command-line options.