The .pmf file is a document file that references GIS data from another source, so it cannot be exported and only viewed using ArcReader:
ArcReader can only read data through a PMF. The PMF supports access to
all standard vector and raster formats supported by ArcGIS. The PMF
does not include the data. Rather, the PMF references the data whether
it is on a local drive, a shared network drive, or an Internet
service. The PMF preserves a live connection to the data, so the
user's data view is dynamic.
If the excel file has x/y or lat/lng coordinates, then you can simply convert it to a .csv and load it into QGIS using the Add Delimited Text Layer button. Once you see the points in the map you can export (Save As) this point event layer to whatever GIS format you would like (e.g. shapefile, file geodatabase...etc).