Here are some examples:
* Confront: to face someone directly
* Conjoin: to join together
* Conclude: to finish or bring to an end
While the prefix "con" can sometimes create a negative meaning, it's not because it means "not". The negativity arises from the context of the word itself.
For example, "condemn" means to criticize strongly. While the "con" in "condemn" doesn't mean "not", the overall meaning of the word is negative.
To express "not", prefixes like "un-", "in-", "non-", or "dis-" are typically used.