The Extra menu is as follows:-

Fit Patch This option creates a new object by warping a flat patch to pass through a number of selected points. More details here.
Count holes This checks each triangle edge to see if there is a matching edge in another triangle. Unmatched edges are collected and sorted into contours representing holes in the surface. An open surface patch will always report at least one "hole" representing its open border. STL data must first be condensed.
Fill smallest hole The contour with the fewest edges (found by the strategy above) is filled with triangles. This strategy is, currently, very simple and will not cope with complex holes.
Fill all holes This recursively applies the above option until there is only one hole left. It then asks whether to fill this (which may be a patch border that you don't want to fill)..
Fill edges If there are two patches, each with a single border edge, this tries to make a closed object by joining the edges together with a strip of triangles.
Delete orphan triangles This will delete any triangle which is not connected, by a common edge, to another triangle.
Smooth (unselected) This smooths the surface of any unmarked region of the object. Repeated application will progressively smooth more. This action will NOT work on the proprietary lsm format. A number is requested, representing a distance, which controls the amount of smoothing.
Dilate selected region This finds the triangles on the border between the selected and unselected areas. It dilates the selected area into the unselected area. One operation selects a single strip of bordereing triangles. Repeated oerations will cause further dilation.
Dilate unselected region As above but dilates in the opposite direction.
Tag seeded surface If the object contains more than one surface patch, a patch can be tagged by placing marker A on the patch and selecting this option. If there is no marker, an arbitrary patch will be tagged.
Tag edge triangles Any triangle containing an "open" edge will be tagged.
Tag bad edge triangles Any triangle with an edge connected to more than one other triangle edge is tagged.
Fix winding Checks adjacent triangle edges to see if the triangles in the surface are all facing the same way. Triangles facing the wrong way are flipped..
Conform to aux This attempts to make part of the current object match the shape of the aux object. A threshold distance (entered by the user) is used to determine which points are morphed..
Conform selected to aux This is like the above option but tagged (unselected) parts of the object are not modified.
Unselect far from aux This tags those parts of the current object which are more than the selected distance from any part of the aux object.
Force condense If an obj file is not properly condensed, this will apply the stl -> obj conversion process to condense it.

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