Pathology telemedicine helps to receive technical guidance from sophisticated experts through media, which assists cancer consultation in hospitals far away. This article proposes a 3D imaging and interactive cutting lines projection system comprising a digital projector and three color cameras. A 3D imaging and the function of projecting interactive markers on specified parts of the sample surface are realized, facilitating remote experts’ pseudo-painting for guiding biological operations. Within each subsystem that works using one camera and the projector, sinusoidal patterns with stripes perpendicular to the baseline are designed to ensure high signal-to-noise ratio 3D results. A phase mapping-based method for projector calibration is proposed by finding the diagonal center of the white squares on the checkboard, avoiding the effect of perspective distortion on the center positioning of circular markers. A point cloud denoising strategy, including phase consistency check and jump region identification, is proposed, allowing the system to perceive detailed morphology without discrete points. Each 3D reconstruction time is less than 3 s, including data acquisition and processing. The accuracy evaluation experiments on the standard plane and sphere show that our system achieves 3D results with a repeatability error of less than $10 \mu \text{m}$ at a field of view of $6 \times 10$ cm, which meets the imaging requirements for pathology telemedicine support.