We can do this with lapply. Subset the columns of interest, loop through them with lapply, assign the output back to the subset of data. Here, we are using c because the outpuf of scale is a matrix with a single column. Using c or as.vector, it gets converted to vector
df[c(3,6)] <- lapply(df[c(3, 6), function(x) c(scale(x)))
Or another option is mutate_at from dplyr
library(dplyr)
df %>%
mutate_at(c(3,6), funs(c(scale(.))))