I'm dealing with cleaning semantic .n3 and rdf files manually from comments and compacting and pretty printing those ones with Regex in C#.
However # is a very common character in semantic files for describing resources.
Example code:
#Processed by Id: cwm.py,v 1.197 2007/12/13 15:38:39 syosi Exp 
        #    using base http://www.prodigi.eu/instances
#  Notation3 generation by
#       notation3.py,v 1.200 2007/12/11 21:18:08 syosi Exp
#   Base was: http://www.prodigi.eu/instances
     @prefix : </ac-schema#> .
    @prefix ins: </instances#> .
    @prefix olanet: <http://www.ibermaticaindustria.com/soluciones/planta-mes-olanet#> .
    @prefix plm: <http://hms.ifw.uni-hannover.de/#> .
    @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
    ins:everyone     a <http://xmlns.com/foaf/0.1/Group>;
         :canSee ins:public;
         rdfs:member <http://127.0.0.1/OslcOlanetProvider/api/producer/01>,
[...]