Physical damages to Si substrate induced by energetic ions from plasma, associated with Si recess, is studied. By using molecular dynamics (MD) simulation, we clarified the structural picture of the damage. By spectroscopic ellipsometry (SE) measurements, we experimentally analyzed damaged layer thickness and energy band structure. Comprehensive analysis of the damage suggests device performance degradation related to basic plasma parameters. The methodology described in this work is necessary in accurate understanding and prediction of plasma-induced damage, e.g., Si recess. Plasma STĨ 50 nm STI Energetic ions Scaling Scaling Si + + Ion-bombardment damage Si recess~2 2nm Si recess + Si substrate Dangling bonds + Si O H Si O H Ions Lattice defect Interstitial atoms