Some deep areas needed special attention to be captured, so after automatic scanning, I manually re-positioned the object using software GUI and scanned those areas.
The final scan looks beautiful
. just look at the quality of the threads in my scan 
watch this video: https://youtu.be/sbWhB2ikTM0
In this video I took too many scans for this part, because I used a script for scanning which was not designed for scanning this object.
Each object needs its own certain strategy for scanning. it is important from where to start scanning and how to handle the process. This is something that can be obtained by experience.