To make one entity semi-transparent you need simply to set its color Alpha component to a value lower than 255. The entity color depends on two factors:

1. Color method (byEntity, byLayer, byParent)
2. Viewport display mode (Shaded, Rendered)

If you are using Rendered display mode for example, the entity color is determined by the relevant Material.Diffuse.A value while the relevant material can be the Entity.Material, the referenced Layer.Material or BlockReference.Material.

Eyeshot features an accurate transparency algorithm based on BSP, this requires a geometry pre-processing stage that could take some time. To improve the speed of the pre-processing stage you can try decreasing the Viewport.Entities.MaxCandidates value. MaxCandidates represents the number of samplings the pre-processing stage takes to simplify the semi-transparent geometry. Increasing it, you increase the probability to get a better frame rate (fps) when you display the model while decreasing it you improve the speed of the pre-processing stage.

Another option to increase your scene frame rate is to set Viewport.Entities.FrontFacingOnly = true, in this case only front facing semi-transparent triangles will be drawn. Combined with visible sharp edges can be a great compromise between speed and accuracy of your scene.

When you set Entity.Visible to false for some semi-transparent entities you need manually to call Viewport.Entities.UpdateBoundingBox() to ensure the geometry pre-processing stage takes place again. UpdateBoundingBox() will also update the shadow and the model bounding box (removing entities just hidden).

Mesh objects with textures or multiple color are still not supported.

If you are still unsatisfied with this approach you might try the Fast Inaccurate Transparency.