Is there any way to peek into a Secondary level cache to see its contents. In addition, can we manipulate the data in the cache ( delete selected data/objects since we no longer will be using it, refresh some stale data if the user already knows that the data was externally modified in the database).
Are there any external tools that can be plugged in to get this kind of access to an already existing cache?

I am not sure if you can change the objects in second level cache ( wonder why you plan on that ) .

But you can sure look the statistics of your second level cache performance

http://www.hibernate.org/hib_docs/v3/api/org/hibernate/stat/Statistics.html

http://www.hibernate.org/275.html