Run-to-run (RtR) control technology has received tremendous interest in semiconductor manufacturing. Exponentially weighted moving average (EWMA), double-EWMA, and internal model control (IMC) filters are recognized methods for online RtR estimation. In this paper, we consider recursive least squares (RLS) as an alternative for online estimation and RtR control. The relationship between EWMA-type and RLS-type estimates is analyzed and verified with simulations. Because measurement delay is almost inevitable in semiconductor manufacturing, we discuss and compare the performance of EWMA, RtR-IMC, and RLS controllers in handling measurement delay and measurement noise for processes with a deterministic drift. An ad hoc solution is proposed to handle measurement delay for processes with time-varying drifts. The results are illustrated through several simulations and a shallow trench isolation (STI) etch process as an industrial example.