Finally, I have got the solution for this problem. To get the answer refer below links.
During implementing this solution, I have observed that static Logger variable in all classes was causing the log merging issue. Here is the good explanation regarding this issue. After reading this, I had to convert all static Logger to class level instance variable.
From
private static final Logger LOGGER = Logger.getLogger(MyApp.class);
To
private final Logger LOGGER = Logger.getLogger(MyApp.class);
After following above changes, logging framework started working fine for me. Now, I can see my all log files contains web app specific logs.
If you want to get detailed analysis on this issue. You can refer this post.