Remove elements based on element content?

Your idea is correct. You need to try to apply it to each item. One option is to use sapply. Check each item str_detectand replace with "", NAotherwise return the value of the item.

library(stringr)
df.clean <- as.dataframe(sapply(df, 
                   function(x)ifelse(str_detect(x, "Not found"), "",x)))
df.clean
# 
# A    B
# 1  A Good
# 2  B     
# 3  C Good
# 4  D     
# 5  E Good
# 6  A     
# 7  B Good
# 8  C     
# 9  D Good
# 10 E   

data

    df <- data.frame(A = rep(c("A", "B", "C", "D", "E"), 2), 
                     B = rep(c("Good","Bad with Not found"),5),
                      stringsAsFactors = FALSE)
df
# A                  B
# 1  A               Good
# 2  B Bad with Not found
# 3  C               Good
# 4  D Bad with Not found
# 5  E               Good
# 6  A Bad with Not found
# 7  B               Good
# 8  C Bad with Not found
# 9  D               Good
# 10 E Bad with Not found