G'day ArunMKumar,

Welcome to the Monastery.

"I also see the .pm files being populated in various tree structures in that lib directory."

Some indication of those "tree structures" would've been helpful. For instance, does the module A::B::C result in

path_to_lib/A/B/C.pm
[download]

or something closer to

path_to_lib/site_perl/5.24.0/.../A/B/C.pm
[download]

Take a look at ExtUtils::MakeMaker. In particular, the "Determination of Perl Library and Installation Locations" section.

You should probably be using PREFIX= and LIB= with perl Makefile.PL (note the uppercase 'L' at the end); not with make install. From the LIB section of "Using Attributes and Parameters":

"LIB should only be set at perl Makefile.PL time but is allowed as a MakeMaker argument."