I have amplified few fragments with Taq polymerase. Now can i remove 3' A overhangs by amplifying again using Phusion DNA polymerase (High fidelity with 3'-5' exonuclease activity) ?
Why didn't you use Phusion in the first place? It would probably work, but the repeated amplification will introduce errors in your amplicons, especially after the Taq step.
You can simply add a proofreading polymerase to the completed PCR and incubate for 10 minutes at 70C. Additional rounds of amplification are not necessary.