InputYamlProcessor.scala

object  {
  
    @throws(classOf[Exception])
    def process(ymlFilename:String):Option[QueryEntities] = {
      
        val ymlFilePath = URLDecoder.decode(ymlFilename, "UTF-8") 
        
        
        Try(Source.fromFile(ymlFilePath).mkString.parseYaml) match {
            case Success(yml) => {
               println("Parsed")
               import CustomYamlProtocol._
               try{ //some logic
                 println( " Input yml :: \n " + yml.prettyPrint)
                
                 val eties:QueryEntities = yml.convertTo[QueryEntities] 
                   
                 /* for (e: Entity <- eties.entities) {
                    println(" columnFamily :  " + e.columnFamily)
                    println(" fromDate :  " + e.fromDate)
                    println(f" toDate :  " + e.toDate)
                  }*/
                  println("done")
                  Some(eties)
                  //Some(yml.convertTo[QueryEntities])
                }catch{
                  case e:Exception => e.printStackTrace()
                        //throw e
                  None
                }
                
               //evalYml(yml);
            }
            case Failure(error) => {
                   error.printStackTrace()
                   println("Unable to parse YAML")
                   None
             }
        }
    
    }
  
}

Tester.scala

case class QueryEntity(columnFamily: String, fromDate: Option[String], toDate: Option[String])
case class QueryEntities(entities: List[QueryEntity])

object Tester{
  def main(args:Array[String]) {
    val ymlFilename ="some.yml";
  val entities: Option[QueryEntities] =  InputYamlProcessor.process(ymlFilename)
        
        for( e: QueryEntities  <- entities ){
          /// this is not working
           //How to access the columnFamily, fromData and toDate ?
        }
  }
}

try remove the type on e

scala> case class Foo(s: String)
defined class Foo
scala> val a: Option[Foo] = Option(Foo("Hello"))
a: Option[Foo] = Some(Foo(Hello))
scala> for (x <- a) { println(x) }
Foo(Hello)