I am quite new to GIS and I have downloaded header files from the reverb website.

My main goal is to get the average NDVI based on a counties polygon shapefile.

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    Too broad. Have you reproject header files? What kind of projection have you in mind? What temporal resolution have MODIS product that you had selected? – aldo_tapia Jan 9 '17 at 10:43

You can use the zonal statistic tools available in ArcGIS spatial analyst or in QGIS zonal statistics plugin. It works with any type of raster layer, but it is safer to make sure that your datasets are in the same coordinate systems (reproject the vector in the CRS of the raster if needed). In ArcGIS, check that the "environment settings" of your zonal stat use the same spatial resolution as your raster, otherwise you could achieve imprecise results.

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