import pandas as pd
import numpy as np

raw_data = {
    'Score1': [42, 52, -999, 24, 73],
    'Score2': [-999, -999, -999, 2, 1],
    'Score3': [2, 2, -999, 2, -999]}
df = pd.DataFrame(raw_data, columns = ['Score1', 'Score2', 'Score3'])

df.loc[:,('Score2', 'Score3')].replace(-999, np.nan, inplace=True)
df