On what basis Directories and Files should be classified (Right now each of my Files are for handling specific section of our application)?

Focus not on files and directories, but on modules. The principal unit of decomposition in Perl is the module.

When designing modules, focus first on the module interface. Perl Best Practices, Chapter 17 (Modules), "Design the module's interface first" advises how to go about this (play testing and so on). For a detailed discussion of software interfaces in general, see On Interfaces and APIs.

What should be the maximum number of lines in a file?

Don't focus on lines in a file. Focus on sound software design. For example:

• Design highly cohesive, loosely coupled modules.
• Ensure modules can be tested in isolation.
• Minimize the exposure of implementation details and avoid global data.

If you do that, code maintenance becomes easier, and none of your files should be grotesquely huge. See also:

• On Coding Standards and Code Reviews
• Writing Solid CPAN Modules