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Something you will cherish :). Please find my suggestion inline with the comments.
With your code:
Time required to calculate in nanoseconds: 3798869988
With mine:
Time required to calculate in nanoseconds: 331338

public class PrimeFactorFinder {
    private static final long NUMBER = 600851475143L;

    public static void main(String[] args) {
        long time = System.nanoTime();
        long result = 0;
        long number = NUMBER;
        for(int i = 2; i <=number; i++) {
            if(number % i == 0 ){
                // 1. You can decrease the number since you do not need it. For 10, you would want to check upto 5 in optimal scenario.
                // 2. Avoiding two divisions with just one unlike yours.
                number = (long)number/i;
                if(isPrime(number)) {
                    result = number;
                    break;
                }
            }
        }
        System.out.println("Result: " + result + "\nTime required to calculate in nanoseconds: " + (System.nanoTime() - time));
    }

    private static boolean isPrime(long l) {
        // Each prime number can be expressed as 6x+1 or 6x-1 except 2 and 3. Eliminate them.
        if(l<4){
            return true;
        }
        if(l%2==0 || l%3==0){
            return false;
        }
        // Best way to shorten the search is to navigate upto the sqrt of the number.
        long sqrt = (long)Math.sqrt(l);
        // That's right. We are incrementing the loop by 6 with 2 and 3 eliminated.
        for(long num = 6 ; num<=sqrt; num+=6) {
            if(l % (num-1) == 0 || (l%(num+1)==0)) { //Possible primes: 6x+1 and 6x-1 
                return false;
            }
        }
        return true;
    }
}

Will modify the previous code soon. For now optimising the primality check.

    private static boolean isPrime(long l) {
        // Each prime number can be expressed as 6x+1 or 6x-1 except 2 and 3. Eliminate them.
        if(l<4){
            return true;
        }
        if(l%2==0 || l%3==0){
            return false;
        }
        // Best way to shorten the search is to navigate upto the sqrt of the number.
        long sqrt = (long)Math.sqrt(l);
        // That's right. We are incrementing the loop by 6 with 2 and 3 eliminated.
        for(long num = 6 ; num<=sqrt; num+=6) {
            if(l % (num-1) == 0 || (l%(num+1)==0)) { //Possible primes: 6x+1 and 6x-1 
                return false;
            }
        }
        return true;
    }

public class PrimeFactorFinder {
    private static final long NUMBER = 600851475143L;

    public static void main(String[] args) {
        long time = System.nanoTime();
        long result = 0;
        long number = NUMBER;
        for(int i = 2; i <=number; i++) {
            if(number % i == 0 ){
                // 1. You can decrease the number since you do not need it. For 10, you would want to check upto 5 in optimal scenario.
                // 2. Avoiding two divisions with just one unlike yours.
                number = (long)number/i;
                if(isPrime(number)) {
                    result = number;
                    break;
                }
            }
        }
        System.out.println("Result: " + result + "\nTime required to calculate in nanoseconds: " + (System.nanoTime() - time));
    }

    private static boolean isPrime(long l) {
        // Each prime number can be expressed as 6x+1 or 6x-1 except 2 and 3. Eliminate them.
        if(l%2==0 || l%3==0){
            return false;
        }
        // Best way to shorten the search is to navigate upto the sqrt of the number.
        long sqrt = (long)Math.sqrt(l);
        // That's right. We are incrementing the loop by 6 with 2 and 3 eliminated.
        for(long num = 6 ; num<=sqrt; num+=6) {
            if(l % (num-1) == 0 || (l%(num+1)==0)) { //Possible primes: 6x+1 and 6x-1 
                return false;
            }
        }
        return true;
    }
}

public class PrimeFactorFinder {
    private static final long NUMBER = 600851475143L;

    public static void main(String[] args) {
        long time = System.nanoTime();
        long result = 0;
        long number = NUMBER;
        for(int i = 2; i <=number; i++) {
            if(number % i == 0 ){
                // 1. You can decrease the number since you do not need it. For 10, you would want to check upto 5 in optimal scenario.
                // 2. Avoiding two divisions with just one unlike yours.
                number = (long)number/i;
                if(isPrime(number)) {
                    result = number;
                    break;
                }
            }
        }
        System.out.println("Result: " + result + "\nTime required to calculate in nanoseconds: " + (System.nanoTime() - time));
    }

    private static boolean isPrime(long l) {
        // Each prime number can be expressed as 6x+1 or 6x-1 except 2 and 3. Eliminate them.
        if(l<4){
            return true;
        }
        if(l%2==0 || l%3==0){
            return false;
        }
        // Best way to shorten the search is to navigate upto the sqrt of the number.
        long sqrt = (long)Math.sqrt(l);
        // That's right. We are incrementing the loop by 6 with 2 and 3 eliminated.
        for(long num = 6 ; num<=sqrt; num+=6) {
            if(l % (num-1) == 0 || (l%(num+1)==0)) { //Possible primes: 6x+1 and 6x-1 
                return false;
            }
        }
        return true;
    }
}

public class PrimeFactorFinder {
    private static final long NUMBER = 600851475143L;

    public static void main(String[] args) {
        long time = System.nanoTime();
        long result = 0;
        long number = NUMBER;
        for(int i = 2; i <=number; i++) {
            if(number % i == 0 ){
                // modifying the number to lessen the loops. Avoiding two divisions with just one.
                number = (long)number/i;
                if(isPrime(number)) {
                    result = number;
                    break;
                }
            }
        }
        System.out.println("Result: " + result + "\nTime required to calculate in nanoseconds: " + (System.nanoTime() - time));
    }

    private static boolean isPrime(long l) {
        // Each prime number can be expressed as 6x+1 or 6x-1 except 2 and 3. Eliminate them.
        if(l%2==0 || l%3==0){
            return false;
        }
        // Best way to shorten the search is to navigate upto the sqrt of the number.
        long sqrt = (long)Math.sqrt(l);
        // That's right. We are incrementing the loop by 6 with 2 and 3 eliminated.
        for(long num = 6 ; num<=sqrt; num+=6) {
            if(l % (num-1) == 0 || (l%(num+1)==0)) { //Possible primes: 6x+1 and 6x-1 
                return false;
            }
        }
        return true;
    }
}

public class PrimeFactorFinder {
    private static final long NUMBER = 600851475143L;

    public static void main(String[] args) {
        long time = System.nanoTime();
        long result = 0;
        long number = NUMBER;
        for(int i = 2; i <=number; i++) {
            if(number % i == 0 ){
                // 1. You can decrease the number since you do not need it. For 10, you would want to check upto 5 in optimal scenario.
                // 2. Avoiding two divisions with just one unlike yours.
                number = (long)number/i;
                if(isPrime(number)) {
                    result = number;
                    break;
                }
            }
        }
        System.out.println("Result: " + result + "\nTime required to calculate in nanoseconds: " + (System.nanoTime() - time));
    }

    private static boolean isPrime(long l) {
        // Each prime number can be expressed as 6x+1 or 6x-1 except 2 and 3. Eliminate them.
        if(l%2==0 || l%3==0){
            return false;
        }
        // Best way to shorten the search is to navigate upto the sqrt of the number.
        long sqrt = (long)Math.sqrt(l);
        // That's right. We are incrementing the loop by 6 with 2 and 3 eliminated.
        for(long num = 6 ; num<=sqrt; num+=6) {
            if(l % (num-1) == 0 || (l%(num+1)==0)) { //Possible primes: 6x+1 and 6x-1 
                return false;
            }
        }
        return true;
    }
}