I have same polygon partially overlapped:
How to delete overlapping and merge it to same area?
I am using QGIS 2.4.0.
First select the two overlapping polygons you want to intersect, enable editing then just merge them using Edit-> Merge Selected Features
and
Save edits.
Alternatively you could try and use the Dissolve
feature.
Take a look at this
The software you are using is key to the best approach. However here are a couple of approaches in two of the most common GIS solutions (other GIS packages are available).
There are other methods such as using clean and build (both in Grass and ArcGIS old Coverage format tools - if they still exist). Dissolving will not retain the boundary between the polygons, which might not be a problem to you.