I have 2 polygons that are over lapped.I want to align the boundaries to match one another.

Send polygon 3 to the ‘Clipper’ port of a Clipper transformer, and send polygons 1 and 2 (or just polygon 2 - use a Tester if needed) to the ‘Clippee’ port then keep the ‘Inside’ part of the result in the Clipper transformer’s output.

Editing - it seems the clipping approach may not do it because not all of the new boundary is overlapped by polygon 3.  In that case using the align edge topology tool in ArcGIS Pro (for example) may be easiest.

I used clippers transformer with align edge tool but the output is not as expected.

Using just the align edge tool with input layers is not giving correct output.

Also using just clipper with input layers is giving output as shown in inspector.

AreaGapAndOverlap while adjustin the tolerance. Also might get better results from the AreaOnAreaOverlayer. Hope this helps!