The advent of sub-aperture computer-numerically controlled (CNC) manufacturing techniques has enabled new opportunities for high-performance optical components and systems. Freeform and other challenging designs are now possible like never before. However, such manufacturing techniques also introduce significant challenges. Mid-spatial frequency (MSF) surface errors are inherent side-effects from sub-aperture manufacturing methods that create prominent constraints on optical design, fabrication, metrology, and performance. Existing methods for specification and measurement of MSF errors in optical systems typically assume isotropic error distributions, which give misleading results for the anisotropic, structured MSF errors that are common with CNC machining. This dissertation investigates MSF errors from three perspectives: (i) Optimization of manufacturing parameters to balance the impacts of MSF errors with manufacturing costs; (ii) Understanding effects of MSF errors on optical performance and creating analysis tools to capture these impacts; and (iii) Development of specification methods for surfaces with MSF errors. Results are addressed through three articles. The first article presents predictive models that provide a means to optimize manufacturing parameters for diamond-machined optics based on their targeted performance. The second article introduces a new, practical tool to characterize the impacts of MSF errors on performance through a novel analysis of the modulation transfer function. The third article presents a novel surface specification method for MSF errors that can be used by designers for optical tolerancing and by manufacturers for acceptance testing. The approaches introduced in the second and the third articles provide a closed-loop for specification, testing, and tolerancing of optical surfaces with MSF errors.