The newest version of my data processing program, let's call it DataReader 2.0...

FileData.java

import java.io.IOException;
import java.io.FileReader;
import java.io.BufferedReader;
import java.io.FileWriter;
import java.io.PrintWriter;
import java.util.Scanner;


public class FileData {
	public static void main(String[] args) throws IOException {
		
		//Creates the scanners and varaibles needed to take user input for the source file.
		System.out.println("Please drag and drop the source data file into the colsole now.");
		Scanner Input = new Scanner(System.in);
		String file_path_in = Input.nextLine();
		
		//Creates the scanners and varaibles needed to take user input for the output file.
		String file_path_out = "NEEDS A DEFAULT LOCATION AND I DIDN'T WANT YOU TO SEE MINE SO ADD ONE";
		Scanner Output = new Scanner(System.in);
		
		System.out.println("The default output file is:");
		System.out.println("			" + file_path_out);
		
		System.out.println("If you would like to change the output file enter '1'");
		int Output_check = Input.nextInt();
		
		if (Output_check == 1) {
			System.out.println("Please drag and drop the new output file into the console now.");
			file_path_out = Output.nextLine();
		} else {
			file_path_out = file_path_out;
		}
		
		
		
		//If for some reason you want to empty the output file each time you process a source file set this to false, otherwise leave it as true.
		Boolean append = true;
		
		//These coordinates define the desired rectangle, Lat1 will be the northern bound, Lat2 the southern, Lon1 the western and Lon2 the eastern.
		double Lat1 = 76.00;
		double Lat2 = 76.8;
		double Lon1 = -69.17;
		double Lon2 = -65.93;
		
		
		//Executes ReadFile if able otherwise throws an exception
		try {
			ReadFile file = new ReadFile(file_path_in, file_path_out, append, Lat1, Lat2, Lon1, Lon2);
			String[] aryLines = file.OpenFile();
		} catch (IOException e) {
			System.out.println(e.getMessage());
		}
	}
}

ReadFile.java

import java.io.IOException;
import java.io.FileReader;
import java.io.BufferedReader;
import java.io.FileWriter;
import java.io.PrintWriter;


public class ReadFile {
	//Variable declarations
	private int processedCount = 0;
	private double ThicknessBound = -9999.00;
	private String path;
	private String path_out;
	private boolean append;
	private double botLat;
	private double topLat;
	private double botLon;
	private double topLon;
	
	public ReadFile (String file_path_in, String file_path_out , boolean append_value, double lowerLat, double upperLat, double lowerLon, double upperLon) {
		path = file_path_in;
		path_out = file_path_out;
		append = append_value;
		botLat = lowerLat;
		topLat = upperLat;
		botLon = lowerLon;
		topLon = upperLon;
	}
	
	//Method to read the file and store it in an array
	public String[] OpenFile() throws IOException {
		
		FileReader fr = new FileReader(path);
		BufferedReader textReader = new BufferedReader(fr);
		
		int numberOfLines = readLines();
		String[] textData = new String[numberOfLines];
		
		for (int i = 0; i < numberOfLines; i++) {
			textData[i] = textReader.readLine();
			
			//Extracts the first two pieces of data and line number
			String fullData = textData[i];
			String[] splitData = fullData.split(",");
			
			String textLat = splitData[0];
			String textLon = splitData[1];
			Double numLat = new Double("0");
			Double numLon = new Double("0");
			
			String testTickness = splitData[3];
			Double numThickness = new Double("0");
			
			//Converts the contents of the text data into doubles
			double Lat = numLat.valueOf(textLat);
			double Lon = numLon.valueOf(textLon);
			double Thickness = numThickness.valueOf(testTickness);
			
			//Checks for data that falls within the user defined bounds
			if (Lat <= topLat && Lat >= botLat && Lon <= topLon && Lon >= botLon && Thickness != ThicknessBound) {
				WriteFile output = new WriteFile(path_out, append);
				output.writeToFile(textData[i]);
				processedCount++;
				System.out.println(Lat + " " + Lon);
			} else {
				processedCount++;
			}
			
			if (processedCount == numberOfLines) {
				System.out.println("There is no more data to process in this file.");
			}
		}
		textReader.close();
		return textData;
	}
	
	int readLines() throws IOException {
		
		FileReader file_to_read = new FileReader(path);
		BufferedReader bf = new BufferedReader(file_to_read);
		
		String aLine;
		int numberOfLines = 0;
		
		while ((aLine = bf.readLine()) != null) {
			numberOfLines++;
		}
		bf.close();
		
		return numberOfLines;
		
	}
}

WriteFile.java

import java.io.FileWriter;
import java.io.PrintWriter;
import java.io.IOException;

public class WriteFile{
	
	private String path;
	private Boolean append_to_file = true;
	
	public WriteFile(String file_path_out , boolean append_value) {
		path = file_path_out;
		append_to_file = append_value;
	}
	
	public void writeToFile(String textData) throws IOException {
		
		FileWriter write = new FileWriter(path , append_to_file);
		PrintWriter print_line = new PrintWriter(write);
		
		//Appends the text file
		print_line.printf( "%s" + "%n" , textData);
		
		print_line.close();
		
	}
}