aakk9999 - 2:08 am on Jan 1, 2013 (gmt 0)
it shows two different url as one http://www.example.com/en and other http://www.example.com/fr
If URLs are as in OP's example, then lets be clear that 'en' and 'fr' are NOT parameters and as such they cannot be set up in WMT. For something to be a parameter in URL, the URL must have ?, the parameter must be after ? and the name of the parameter is to the left of the = sign.
If the content of two URLs given as OP's example is the same (that is, it is also in the same language), then either there is no equivalent content set up in CMS for alternate language so both languages pick up a "default" content, or there is a serious issue on how URL Rewrite is handled on the site.
If the content means the same, but is in different languages, then (as Robert said in his post above) this is not a duplicate content.
If you decide to go for noindex method, and if the content is taken from the same CMS source in admin, then after setting up noindex, you better check that the other URL is NOT noindexed by the virtue of taking the content from the same place in CMS.