You can exclude classes from instrumentation. Then they should not appear on reports. See exclude statements below.
You can also ignore calls to some methods. See ignore statement below.
If you are using maven, see maven plugin manual.
<configuration>
<instrumentation>
<ignores>
<ignore>com.example.boringcode.*</ignore>
</ignores>
<excludes>
<exclude>com/example/dullcode/**/*.class</exclude>
<exclude>com/example/**/*Test.class</exclude>
</excludes>
</instrumentation>
</configuration>
And for ant see this.
<cobertura-instrument todir="${instrumented.dir}">
<ignore regex="org.apache.log4j.*" />
<fileset dir="${classes.dir}">
<include name="**/*.class" />
<exclude name="**/*Test.class" />
</fileset>
<fileset dir="${jars.dir}">
<include name="my-simple-plugin.jar" />
</fileset>
</cobertura-instrument>