Once you found how to get your data into some 3d vertex information, I would 
advice to have a look at mesh lab. It offers a lot of filters just as what you 
are looking for.

> Not so long ago we discussed exporting the data and rendering the 3D image in 
> another software package.  Yeti even implemented a vtk export filter.  If you 
> then import into something like paraview you can filter the data as you 
> require...  There is a learning curve for pretty much an visualization 
> software though...
> 
> Scott
> 
> 
> On Fri, Jan 18, 2013 at 1:45 PM, David Nečas (Yeti) <[email protected]> wrote:
>> On Fri, Jan 18, 2013 at 02:37:12PM -0500, Collin Becker wrote:
>> > I am trying to decrease the resolution in my 3d image.  In other words,
>> > when I make a 3d image, the image is very rough because every single data
>> > point is being included and the image does not look very clean.  Other
>> > software I have allows you to increase or decrease the "level of detail" in
>> > the 3d image to help you smooth out the 3d image for easier viewing.  I
>> > cannot figure this out though in Gwyddion.
>> 
>> In Gwyddion the resolution in all views is the resolution of the image.
>> I would say that the necessity to mess up with resolution in 3D views is
>> another indication that 3D projection is a poor data visualisation
>> method – but that would be just my hatred of 3D speaking...
>> 
>> You can use Data Process → Basic Operations → Scale to reduce the
>> resolution and/or a smoothing filter such as Gaussian in Filters tool.
>> Binning would be probably the most natural operation when one wants
>> simultaneous resolution reduction and heavy smoothing but binning is not
>> implemented.
>> 
>> Regards,
>> 
>> Yeti
>> 
>> 
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