FCB::Open failed: Could not open file The machine was restarted while I was shrinking a database and since then the SQL Server (MSSQLSERVER) not starting. After reading the blogs I replaced the master.mdf and  mastlog.ldf files from the templates folder with the same file, assuming master database was corrupted as I was shrinking this.

However the problem remains and the error log file gives the following message,

Starting up database 'msdb'.
Starting up database 'mssqlsystemresource'.
Error: 17204, Severity: 16, State: 1.
FCB::Open failed: Could not open file E:\sql12_main_t.obj.x86Release\sql\mkmastr\databases\mkmastr.proj\MSDBData.mdf for file number 1.  OS error: 3(The system cannot find the path specified.).
Error: 5120, Severity: 16, State: 101.
Unable to open the physical file "E:\sql12_main_t.obj.x86Release\sql\mkmastr\databases\mkmastr.proj\MSDBData.mdf". Operating system error 3: "3(The system cannot find the path specified.)".
Error: 17207, Severity: 16, State: 1.
FileMgr::StartLogFiles: Operating system error 2(The system cannot find the file specified.) occurred while creating or opening file 'E:\sql12_main_t.obj.x86Release\sql\mkmastr\databases\mkmastr.proj\MSDBLog.ldf'. Diagnose and correct the operating system error, and retry the operation.
File activation failure. The physical file name "E:\sql12_main_t.obj.x86Release\sql\mkmastr\databases\mkmastr.proj\MSDBLog.ldf" may be incorrect.
The resource database build version is 12.00.2000. This is an informational message only. No user action is required.
Starting up database 'model'.


I can clearly say that there is no E:\ partition on my machine. Can you please help me to fix the path which I assume is the error now?
You replaced master with the one that comes from the SQL Server build process. This one is pointing to the release build mkmaster folders for msdb database. As msdb is no a system database, you should be able to start the engine, connect to it, detach msdb and re-attach the correctly located one. But this is not the correct process. The correct process is described in Rebuild System Databases, and involves running setup.exe:

Setup /QUIET /ACTION=REBUILDDATABASE ...