Hi Prashanth,
With SAP HANA you will have to use any of the ETL tool like BODS, SLT or any third party ETL tool like Informatica which can connect to HANA over JDBC / ODBC connectivity and perform data insert operations.
You can also generate CSV file dumps for your 40 tables and load them to HANA using flat file upload interfaces.
Since HANA cannot connect directly to SQL server, you will have to use the ETL tool.
If possible, you can also create your custom application in .NET (Dot NET) which can connect to HANA over ODBC (or JDBC) and perform the inserts reading data from the MSSQL tables.
Regards,
Ravi