Yes, you can. DeepSea Obfuscator comes with a NAnt task.
Here's an example on how you can use it.
<loadtasks assembly="DeepSea.NAnt.dll" />
<deepsea todir="${testdir}\Out" mapfile="HelloWorld.dsomap" verbose="true">
<assemblies basedir="${testdir}">
<include name="HelloWorld.exe"/>
</assemblies>
</deepsea>1 <loadtasks assembly="DeepSea.NAnt.dll" />
2 <deepsea todir="${testdir}\Out" mapfile="HelloWorld.dsomap" verbose="true">
3 <assemblies basedir="${testdir}">
4 <include name="HelloWorld.exe"/>
5 </assemblies>
6 </deepsea>