Dear Mritunjay,
DREAM3D-NX currently does NOT have the synthetic building capability. You will have to use DREAM.3D version 6.5.171 to create synthetics.
The blue areas you are seeing is because the virtual volume is orthogonal prism shape. The pipeline you ran has the filters necessary to mask out parts of the virtual volume so that grains are not generated there but since those voxels are part of the virtual volume they will appear. You can visually remove them by using a “Threshold” filter in preview and setting the threshold to featureId >=1. This will remove the blue section.
Within DREAM.3D itself you could create a surface mesh using the appropriate mask and at the end of the pipeline the blue areas would not be included in the surface mesh.
It all really depends on what you want to do with the synthetic model.