Efficient algorithm to filter off points from a point cloud
You should use a set data structure for your subset-list. This would allow querying if it contains a given point in constant time.

Your function, as python-like pseudocode:

def FilterPoints(master, subset):
    # take the list and convert it to a set ( O(|subset|)
    subset_set = set(subset)
    # iterate through master and and the points that are not in subset O(|master|)
    filtered_list = [p for p in master if p not in subset_set]
    return filtered_list


Some points:


If master is larger than subset, the algorithm will be $\mathcal O(|master|)$ 
The equivalent of set in C# should be HashSet