Modified silicon-on-insulator (SOI) substrates having a trap rich layer, and methods for making such modifications. The modified regions eliminate or manage accumulated charge that would otherwise arise because of the interaction of the underlying trap rich layer and active layer devices undergoing transient changes of state, thereby eliminating or mitigating the effects of such accumulated charge on non-RF integrated circuitry fabricated on such substrates. Embodiments retain the beneficial characteristics of SOI substrates with a trap rich layer for RF circuitry requiring high linearity, such as RF switches, while avoiding the problems of a trap rich layer for circuitry that is sensitive to accumulated charge effects caused by the presence of the trap rich layer, such as non-RF analog circuitry and amplifiers (including power amplifiers and low noise amplifiers).