You can chain methods together like this.

      for(int i = 0; i < users.size(); i++){
         if(idNum == users.get(i).getIdNum()){
            final Student temp = users.get(i);
            System.out.println("Student with an ID of " + temp.getIdNum() + " has an age of " + temp.getAge());
         }
      }

Here, I chained users.get(i) to get the Student at index i, then I call getIdNum(), which fetches the ID from that Student that I just fetched.

Then, I perform a == comparison --> Is the ID that the user entered the same as the ID from this particular Student I am looking at?

If the result is true, then I call users.get(i) again, which fetches that same Student again, and then I store that into a temporary Student variable called temp. temp is now referencing that Student on the ArrayList that passed the ID check.

Then, I take temp, and use the getIdNum() and getAge() methods that it has (because temp is an instance of Student, and Student has those methods), and use them to create a message that I print onto the command line.

Here is a complete, runnable example.

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Scanner;

public class SOQ_20220514
{

   public static class Student {
      private String lName;
      private int idNumber;
      private int age;
   
      public Student() {
         lName = "";
         idNumber = 0;
         age = 0;
      }
      public Student(String l, int i, int a) {
         lName = l;
         idNumber = i;
         age = a;
      }
   
      public void setName(String last) {
         lName = last;
      }
   
      public String getName() {
         return lName;
      }
   
      public void setIdNum(int num) {
         idNumber = num;
      }
   
      public int getIdNum() {
         return idNumber;
      }
   
      public void setAge(int a) {
         age = a;
      }
   
      public int getAge() {
         return age;
      }
   }

   public static void main(String[] args) throws IOException {
      String file = "studentData.txt";
      Scanner reader = new Scanner(file);
   
      ArrayList<Student> users = readFile(file);
      Student s = new Student();
      users.add(s);
   
   
      Scanner input = new Scanner(System.in);
    //user enters idNumber to display age
      System.out.println("Enter ID Number"); //exception handling to be added
      int idNum = input.nextInt();
   
   //this part is where I'm stuck 
      for(int i = 0; i < users.size(); i++){
         if(idNum == users.get(i).getIdNum()){
            final Student temp = users.get(i);
            System.out.println("Student with an ID of " + temp.getIdNum() + " has an age of " + temp.getAge());
         }
      }
   
   }
//METHOD FOR READING FILE
   public static ArrayList<Student> readFile(String file)throws IOException{
      Scanner reader = new Scanner(new File(file));
   
      ArrayList<Student> list = new ArrayList<Student>();//creates ArrayList with student object
   
      reader.nextLine();//skips first line
      while(reader.hasNext()){//splits all text in the file into words
         String lName = reader.next();
         int idNum = reader.nextInt();
         int age = reader.nextInt();
      
         Student users = new Student(lName ,idNum, age); 
         list.add(users);
      }
    
      return list;
   
   }//end method

}

The Answer by davidalayachew looks correct. For fun, here is an alternative.

Streams

Provide input data. I will simulate a file with a String as textual input.

String input =
        """
        Josh,2134,19
        Smith,5256,21
        Rogers,9248,19
        Andrew,7742,20     
        """;

Define a Student class to hold data. If the main purpose of this class is to transparently and immutable communicate data, use a record. The compiler implicitly creates the constructor, getters, equals & hashCode, and toString.

record Student( String name , int id , int age ) { }

Note that we can declare a record locally, within a method. Or declare nested in another class, or separately on its own.

Next we do a bunch of work in a single statement by using streams.

First we make a stream of each line in our input text. By calling String#lines, we get a Stream< String >, a series of elements of type String.

For each one of those lines, we call Stream#map to create another stream. We split each line by COMMA character to get a string arrays, String[]. Each array has three elements, the three pieces of info in each line.

For each string array of line parts, we call Stream#map yet again to make yet another stream. This third stream will be a stream of Student objects. We produce each Student object by taking the three parts of the line, parsing the 2nd and 3rd into int values, and feeding all 3 into the constructor of our Student record. The result is a Student, one student object after another, forming a third stream.

Lastly, we collect the Student objects produced by that third stream into a list.

List < Student > students =
        input
                .lines()                            // First stream, of `String` objects, one for each line in our source text.
                .map( line -> line.split( "," ) )   // Second stream, of `String[]` objects. 
                .map( lineParts ->                  // Third stream, of `Student` objects produced by the three parts of each line of input text.
                        new Student(
                                lineParts[ 0 ] ,
                                Integer.parseInt( lineParts[ 1 ] ) ,
                                Integer.parseInt( lineParts[ 2 ]
                                )
                        )
                )
                .toList();

Your goal is to change the age of each student. To do that with immutable objects (records), we can define a method that returns a new object based on values from the original. So we add a withAge method. We use the word with per naming conventions established by the java.time classes.

record Student( String name , int id , int age )
{
    Student withAge ( int age ) { return new Student( this.name , this.id , age ); }
}

Make your modified ages.

List < Student > results = new ArrayList <>( students.size() );
for ( int i = 0 ; i < students.size() ; i++ )
{
    Student student = students.get( i );
    results.add( student.withAge( i ) );
}

Here is that entire example class, for your copy-paste convenience.

package work.basil.example.text;

import java.util.ArrayList;
import java.util.List;

public class App
{
    public static void main ( String[] args )
    {
        App app = new App();
        app.demo();
    }

    private void demo ( )
    {
        String input =
                """
                Josh,2134,19
                Smith,5256,21
                Rogers,9248,19
                Andrew,7742,20     
                """;

        record Student( String name , int id , int age )
        {
            Student withAge ( int age ) { return new Student( this.name , this.id , age ); }
        }

        List < Student > students =
                input
                        .lines()
                        .map( line -> line.split( "," ) )
                        .map( lineParts ->
                                new Student(
                                        lineParts[ 0 ] ,
                                        Integer.parseInt( lineParts[ 1 ] ) ,
                                        Integer.parseInt( lineParts[ 2 ]
                                        )
                                )
                        )
                        .toList();

        List < Student > results = new ArrayList <>( students.size() );
        for ( int i = 0 ; i < students.size() ; i++ )
        {
            Student student = students.get( i );
            results.add( student.withAge( i ) );
        }

        System.out.println( "students = " + students );
        System.out.println( "results = " + results );
    }
}

When run.

students = [Student[name=Josh, id=2134, age=19], Student[name=Smith, id=5256, age=21], Student[name=Rogers, id=9248, age=19], Student[name=Andrew, id=7742, age=20]] results = [Student[name=Josh, id=2134, age=0], Student[name=Smith, id=5256, age=1], Student[name=Rogers, id=9248, age=2], Student[name=Andrew, id=7742, age=3]]