The reduction or elimination of leakage of hydraulic fluid from fluid power systems is considered a fundamental prerequisite for the expanded use of fluid power. There is also a need to reduce seal friction to both reduce energy dissipation and eliminate control problems. These seals are developed through empirical means at the present time, since the fundamental physics of seal operation has been unclear. This research develops numerical models for analyzing reciprocating hydraulic rod seals with various rod surfaces. These models consist of coupled fluid mechanics, contact mechanics and deformation analyses. Both flooded and starved lubrication boundary conditions are applied. For seals with a smooth rod and a plunge-ground rod, the model combines a 1-D finite volume Reynolds equation solver with a 2-D axisymmetric finite element deformation and static contact mechanics analyses, and a Greenwood-Williamson contact mechanics analysis with rod motion. Leakage and friction, along with sealing zone details with the plunge-ground rod are compared with those with the smooth rod. The influence of rod surface finish on seal performance is investigated and explained, under both flooded and starved conditions For seals with a micro-patterned rod, the model consists of finite volume Reynolds equation solver, finite element deformation and static contact mechanics analyses and a Greenwood-Williamson dynamic contact mechanics analysis. This model is able to handle rod surface pattern with 3-dimensional geometrics. Simulations with different micro-pattern geometries are performed to analyze the fundamental mechanism of surface pattern effects on seal operation. Again, both flooded and starved conditions are applied and the results for both cases are compared and analyzed.