Many different utilities can be used for data preparation, in the example I will use the following free software:
1) 3DEM viewer : available at http://www.visualizationsoftware.com/3dem.html (viewer - format converter)
In the following examle UTM DEM dataset is converted to WGS84 Lat/long. This example is a part of Topo_creator page. Similar to other projections.
1660095.DEM.SDTS.TAR ( 10m UTM DEM) data set was downloaded from the Internet and converted to hunter.dem with sdts2dem.exe utility. File size is ~9Mb
Observe the hunter.dem with 3DEM viewer:
We see that the map contains zeros at border area, they must be removed. Select (write on a piece of paper) area we can trust (to be sure that zero borders are out of this area), say: -74.2496, -74.1273, 42.2491, 42.1259.
For example, our task is to reproject the UTM DEM to WGS84 Lat/long, cut zeros at the edges and create height matrix (or GeoTiff image) of 512x512 size.
We must cut edges of our hunter.dem to selected area (-74.2496, -74.1273, 42.2491, 42.1259), convert data to WGS84 Lat/Long, resample to have 512 rows and 512 columns.
This is one step operation with gdalwarp utility):
gdalwarp.exe -t_srs WGS84 -rcs -ts 512 512 -te -74.2494 42.1263 -74.1259 42.2493 hunter.dem hunter.tif
see description of gdalwarp.exe for all set of parameters. Here we use:
-t_srs WGS84 (WGS84 Lat/Long projection)
Conversion takes several seconds. Here is the result, image is stretched horizontally compared to original data, this is due to UTM-Lat/Long conversion.
GeoTiff can be then saved to different formats with 3DEM viewer, or alternatively, another format of output file can be choosen with the "-of " option of gdalwarp (see example on 2D page).