A method of manufacture of an integrated circuit packaging system includes: forming a rounded interconnect on a package carrier having an integrated circuit attached thereto, the rounded interconnect having an actual center; forming an encapsulation over the package carrier covering the rounded interconnect; removing a portion of the encapsulation over the rounded interconnect with an ablation tool; calculating an estimated center of the rounded interconnect; aligning the ablation tool over the estimated center; and exposing a surface area of the rounded interconnect with the ablation tool.