Hi Rishav,
3.1 and 4.1 are different platforms, hence you cannot directly upgrade a 3.1 system to 4.0 or 4.1
you have to first check your hardware requirement and software specifications as per the PAM guide available at service market place. For guides related to install and configuration of BI 4.1, go through SAP BusinessObjects Business Intelligence platform 4.1 – SAP Help Portal Page
Once you have done that, start a full build installation of BI 4.1 SP4 on the server machine.
Once the installation is complete using default db ( or you can choose to point the SIA to a blank new schema and do the installation )
Once done, check if SIA is up and running, login to CMC and check if all servers are up and running as well.
Post that, using the UMT tool, you can migrate your data to the BI 4.1 system.
To do that, check the administrator guide.
Hope this helps
Regards.
Atul B