By default cPanel does not show hidden files for security reasons. So you have to make few changes in setting to make hidden files visible. In my case I wanted to access ".htaccess" file in root folder to change as per newly created website.
Follow below steps to make hidden file visible:
1) You need to login to cPanel using credentials.
2) Navigate to "File manager" in "File" section.
3) In file manager you will see file listing with setting button at the right top corner of the page.
4) Click on "Settings" button, which will open an popup like below:
5) Check on "Show Hidden Files (dotfiles)" and click "Save" button.
Now you will be able to access hidden files in directory.