I'll take a guess that you are reading in a pdf file and that it is interpreted OK including some header and footer areas.
Normally you might hope to be able to define a trap for the other templates which mean the Page Header and Footer areas would not be selected.
If that is not possible you can maybe deal with the Page Header by defining a template that includes all the page header rows and a trap that only applies to those rows. This template does not require fields if you don't need any of the data from those rows.
Monarch will skip over those lines of the report mapped as Page Header lines when it is processing.
In theory you need to do something similar for the footer but that can often be complicated if you cannot work out a unique trap. The Footer Template functionality is not quite as specific as the Page Header functionality described above but does expect to be at the end of a 'record'. However if it's position cannot be clearly identified by a unique trap definition things may get a little more complicated.
An example of the sort of layout you are dealing with would be helpful (the text extracted form the pdf is what is required) if you are still stuck. These things can often be very specific to the report format.