This paper reports two virtual pointer alignment experiments carried out using a stereoscopic augmented reality interface. The purpose was to evaluate users' sensitivity to surface texture, target position at designated probe points on a cylinder real object surface, virtual pointer form and binocular disparity. The results confirmed the main findings from a previous study: that both surface texture and target position have significant influences. Subjective evaluation of virtual pointer form revealed that a three dimensional pointer is preferred over one and two-dimensional pointers. The contributions of size cue and resolution to binocular disparity effects are also discussed in relation to interface design issues for augmented reality applications.