My query is : After generating NDVI or other indices in SNAP from one Sentinel 2 image and masking out the result to 2 hectares size of land, the result looks like pixels or boxes. Like it is pixelated. Any suggestions to fix it in SNAP. Thanks in advance for your explanation.
two hectares are only 20x10 pixels. So it is natural that it pixelated.
What you can do is to increase the resolution. You can upsample the image to e.g. 2000x1000 pixels and use a linear interpolation method. You can do this with the Resampling operation.
But with this you get artificial values which have not been measured.