Automated point's value extraction from SAR 1 / extraction and projection for sea ice

[fargasht]

I need to extract the SAR images to process in Matlab for sea ice but I have a projection problem.
I have used the Ellipsoid train correction and directly I am using GeoTIFF to extract them with an automated process. But I got a problem to read images in Matlab as they are not fitting together with other layers.(With the same method works for other GeoTIFFs)
I tried to use Geometric Operation => Mosaicing then after to solve the projection problem or in some way geocoding them. But I have more than 100 images to process and that was not helpful again.
=>>>>>>>
The purposes;

1. Export the image in GeoTIFF to open in MATLAB
2. Extract the values of SAR for points
   Problems;
3. The reprojection in SNAP makes the image bounding bigger(empty pixels around)
4. The subset is not possible in SANP for points (just polygons possible)

So, would it be possible to give me some suggestions to fix this problem?!
Thank you in advance,

[ABraun]

Is it an option to re-project the shapefile so it matches the coordinates of the SAR images?

Maybe you can add some screenshots to illustrate your problem.