MODIS reprojection

Hi,

I am working with MODIS aerosol products (hdf files), especifically MOD04_L2. I need to get the data for an specific location (pixel where my point of interest is) and once I have find it, select an area of 50 x 50 km (5 x 5 pixels) centered on that one.

However, as my pixel of interest is further from the center of the image (swath) its size is bigger than 10 x 10 km. Do you know how can I solve this problem? I have tried to reproject but I am not able to get the data once I have done this. I have files of latitude, longitud and my parameter of interest.

Help please! Thanks!