Speaking about a url rewrited site, you can segment by search engine into CONTENT -> CONTENT DRILLDOWN report, isolate your directory then look at search engine traffic (by segmentation or advanced segmentation).

Another way is to create a duplicate profile and add a search-engine-only include filter and a "include only traffic to a specific directory" filter.

• Open the Advanced Segments (on the top right corner)
• click on "Create a new advanced" segment
• Select Content -> Page

• Set the segment condition with “Starts with”

• insert in the value field the name of the directory that you need analyse the visits.

• Save and apply the segment

• Finally, browse the Google Analytics account to see the visits from search engine at your directory