We study the mass of asymptotically flat 3-manifolds with boundary using the method of Bray-Kazaras-Khuri-Stern [5]. More precisely, we derive a mass formula on the union of an asymptotically flat manifold and fill-ins of its boundary, and give new sufficient conditions guaranteeing the positivity of the mass. Motivation to such consideration comes from studying the quasi-local mass of the boundary surface. If the boundary isometrically embeds in the Euclidean space, we apply the formula to obtain convergence of the Brown-York mass along large surfaces tending to ∞ which include the scaling of any fixed coordinate-convex surface.Proposition 1.1. Let (M, g) be an asymptotically flat 3-manifold with boundary Σ. Let u be a harmonic function on M which is asymptotic to one of the asymptotically flat coordinate functions at infinity. Let Σ t = u −1 (t) be the level set of u and ν be the infinity pointing unit P. Miao acknowledges the support of NSF Grant DMS-1906423.