You can use some GIS softwares like ArcGIS 3D engine or QGIS, these softwares have the possibility to represent 3d objects or to transform 2D object (vector or raster layer) to a 3D entity;
The other possibility is to code your own visualisation platforme using OpenGL for example.
we don't know much about the content of your database and the characteristics of your geo-data and about the visualization aims, so it's difficult to give an answer...
However, writing your own OpenGL code would be very very laborious and does not make sense!!
So I would recommend to use an existing GIS-system, e.g. one of those systems mentioned by Mehdi, i.e. QGIS (which is Open-Source and free) or ArcGIS.
In case, you want do do some programming by yourself, this Java-based framework could be useful:
According on your dataset, a simple OpenGL program may help., this solution would give you all the freedom you need to interact with the data. Of course some knowledges about OpenGL are required.
I know GRASS can be tricky to get your head around initially, but it is quite powerful and customisable. Use the following link to see a few screen shots and a description/manual of how to use NVIZ - https://grass.osgeo.org/screenshots/3D/
Very useful software is mentioned above ArcScene (from ArcGIS), which is good in 3D or 2D exporting files. Also usable software is Global Mapper, which operates many raster formats and DEMs (ie. LiDAR data). If You looking for software only to 3D - interesting propose is Surfer; well - there are many GIS and visualising data programms.