I am not really sure about what exactly you need to do.
Do yours 100 grid polygons snap to pixels of raster? (1 polygon = 1 pixel)
And do you need to extract raster values into polygon grid?
If it is sufficient for you only to extract raster pixel data and do have it in one table, you can firstly (in ArcGIS):
convert raster to points (
conversion->From Raster->Raster to Point)
extract raster pixel values into this new points.shp
Spatial analysis->Extraction->Extract Values to Points) or if you have multiple rasters use
Extract Multi Values to Points (Warning! with zero value it doesnt work very well!)
export attribute table with values for each pixel (look maybe here: http://www.geoplanit.co.uk/?p=21)
If you would like to use polygons, dont you want to try convert Raster to Polygon? (
conversion->From Raster->Raster to Polygon) and overlay it than with your 100 polygons grid?
Hope it helps, or thy to specify your question