I assume you are using the Weka Explorer (GUI). To apply the filter to specific attributes do the following.
Step 1: Select your filter in the preprocess tab
Step 2: Click on the box to the right of the "Choose" button (a new window opens)
Step 3: In the attributeIndices box enter your custom ranges
If you select the "More" button in the filter window you will get an explanation of the different options and the values you can supply.
In your particular case, the filter is by default applied to the first through last attributes. You should change the range to reflect your personal needs.
====Edit====
If you are using the Java API, the following code will point you in the right direction.
import weka.core.Instances;
import weka.filters.Filter;
import weka.filters.unsupervised.attribute.NumericToNominal;
public class Main {
public static void main(String[] args) throws Exception
{
//load training instances
Instances originalTrain= //...load data with numeric attributes
NumericToNominal convert= new NumericToNominal();
String[] options= new String[2];
options[0]="-R";
options[1]="1-2"; //range of variables to make numeric
convert.setOptions(options);
convert.setInputFormat(originalTrain);
Instances newData=Filter.useFilter(originalTrain, convert);
System.out.println("Before");
for(int i=0; i<2; i=i+1)
{
System.out.println("Nominal? "+originalTrain.attribute(i).isNominal());
}
System.out.println("After");
for(int i=0; i<2; i=i+1)
{
System.out.println("Nominal? "+newData.attribute(i).isNominal());
}
}
}