There is no manual crop module, but there are options to crop each image differently using the Crop module. You can crop each image into objects identified within that image, for example (which would scale to the size of the image) or to a corresponding template that you've loaded. You can also manually outline an ellipse or rectangle to crop for each image, by selecting either Ellipse or Rectangle (rather than a specific object) as the shape you would like to crop into, then selecting Mouse as the option for how you would like to crop. Finally, make sure to select Individual for how you the cropping pattern should be applied. In this mode, you will be presented with each image and you get to click around to define the cropping shape.
A similar method of manual identification is possible using IdentifyPrimManual. Every cycle, you are presented with the image and can click around to define the objects.
As of now, there is no easy way to go from objects automatically identified in IdentifyPrimAuto to adding or deleting them, as you suggest (though we've had other requests!). You can certainly convert your objects to an image, for example, then outline each one that you'd like to keep manually in IdentifyPrimManual- but adding objects is a bit trickier. It's best to just start from manual segmentation in that case.